Sample records for cd40l dna combined

  1. Mechanisms of Nifedipine-Downregulated CD40L/sCD40L Signaling in Collagen Stimulated Human Platelets.

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    Tso-Hsiao Chen

    Full Text Available The platelet-derived soluble CD40L (sCD40L release plays a critical role in the development of atherosclerosis. Nifedipine, a dihydropyridine-based L-type calcium channel blocker (CCB, has been reported to have an anti-atherosclerotic effect beyond its blood pressure-lowering effect, but the molecular mechanisms remain unclear. The present study was designed to investigate whether nifedipine affects sCD40L release from collagen-stimulated human platelets and to determine the potential role of peroxisome proliferator-activated receptor-β/-γ (PPAR-β/-γ. We found that treatment with nifedipine significantly inhibited the platelet surface CD40L expression and sCD40L release in response to collagen, while the inhibition was markedly reversed by blocking PPAR-β/-γ activity with specific antagonist such as GSK0660 and GW9662. Meanwhile, nifedipine also enhanced nitric oxide (NO and cyclic GMP formation in a PPAR-β/-γ-dependent manner. When the NO/cyclic GMP pathway was suppressed, nifedipine-mediated inhibition of sCD40L release was abolished significantly. Collagen-induced phosphorylation of p38MAPK, ERK1/2 and HSP27, matrix metalloproteinase-2 (MMP-2 expression/activity and reactive oxygen species (ROS formation were significantly inhibited by nifedipine, whereas these alterations were all attenuated by co-treatment with PPAR-β/-γ antagonists. Collectively, these results demonstrate that PPAR-β/-γ-dependent pathways contribute to nifedipine-mediated downregulation of CD40L/sCD40L signaling in activated platelets through regulation of NO/ p38MAPK/ERK1/2/HSP27/MMP-2 signalings and provide a novel mechanism regarding the anti-atherosclerotic effect of nifedipine.

  2. High sCD40L levels Early After Trauma are Associated with Enhanced Shock, Sympathoadrenal Activation, Tissue and Endothelial Damage, Coagulopathy and Mortality

    DEFF Research Database (Denmark)

    Johansson, P I; Sørensen, A M; Perner, A;


    was associated with enhanced tissue and endothelial damage (ISS, hcDNA, Annexin V, syndecan-1, sTM), shock (pH, SBE), sympathoadrenal activation (adrenaline) and coagulopathy evidenced by reduced thrombin generation (PF1.2), hyperfibrinolysis (D-dimer), increased APTT and inflammation (IL-6) (all p......Background: Severe injury activates the sympathoadrenal, hemostatic and inflammatory systems, but a maladapted response may contribute to poor outcome. Soluble CD40L is a platelet derived mediator that links inflammation, hemostasis and vascular dysfunction. Objectives: To investigate......-complex, antithrombin, protein C, activated Protein C, sEPCR, TFPI, vWF, fibrinogen, FXIII), fibrinolysis (D-dimer, tPA, PAI-1) and inflammation (IL-6, sC5b-9). We compared patients stratified by median sCD40L level and investigated predictive values of sCD40L for mortality. Results: High circulating sCD40L...

  3. Is Delayed Pressure Urticaria Associated with Increased Systemic Release of sCD40L?

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    T. Jasinska


    Full Text Available Background. Elevated levels of soluble CD40 Ligand (sCD40L were found in serum but not in plasma of patients with chronic spontaneous urticaria (CU. What is important is that sCD40L has proinflammatory properties, and its elevated plasma level may indicate increased risk of cardiovascular events. These observations should stimulate further evaluation of sCD40L in different forms of urticaria. Aim. In the present study, sCD40L plasma level was investigated in delayed pressure urticaria (DPU. Methods. As platelets are predominant and variable sources of sCD40L, we investigated sCD40L concentration in platelet-poor plasma (PPP, which seems the best way to minimize the potential contribution of these cells to the ligand level. Results. Plasma sCD40L concentration was significantly increased in the DPU group compared to the healthy controls. Conclusions. It seems that DPU is associated with increased systemic release of sCD40L, which is believed to derive predominantly from activated platelets. The present study as well as the earlier contributions suggest that distinct cells activity, including platelets, may be identified in different types of urticaria.

  4. Rac1 regulates platelet shedding of CD40L in abdominal sepsis. (United States)

    Hwaiz, Rundk; Rahman, Milladur; Zhang, Enming; Thorlacius, Henrik


    Matrix metalloproteinase-9 (MMP-9) regulates platelet shedding of CD40L in abdominal sepsis. However, the signaling mechanisms controlling sepsis-induced shedding of CD40L from activated platelets remain elusive. Rac1 has been reported to regulate diverse functions in platelets; we hypothesized herein that Rac1 might regulate platelet shedding of CD40L in sepsis. The specific Rac1 inhibitor NSC23766 (N6-[2-[[4-(diethylamino)-1-methylbutyl] amino]-6-methyl-4-pyrimidinyl]-2 methyl-4, 6-quinolinediamine trihydrochloride) was administered to mice undergoing cecal ligation and puncture (CLP). Levels of CD40L and MMP-9 in plasma, platelets, and neutrophils were determined by use of ELISA, western blot, and confocal microscopy. Platelet depletion abolished the CLP-induced increase in plasma levels of CD40L. Rac1 activity was significantly increased in platelets from septic animals. Administration of NSC23766 abolished the CLP-induced enhancement of soluble CD40L levels in the plasma. Moreover, Rac1 inhibition completely inhibited proteinase-activated receptor-4-induced surface mobilization and secretion of CD40L in isolated platelets. CLP significantly increased plasma levels of MMP-9 and Rac1 activity in neutrophils. Treatment with NSC23766 markedly attenuated MMP-9 levels in the plasma from septic mice. In addition, Rac1 inhibition abolished chemokine-induced secretion of MMP-9 from isolated neutrophils. Finally, platelet shedding of CD40L was significantly reduced in response to stimulation with supernatants from activated MMP-9-deficient neutrophils compared with supernatants from wild-type neutrophils, indicating a direct role of neutrophil-derived MMP-9 in regulating platelet shedding of CD40L. Our novel data suggest that sepsis-induced platelet shedding of CD40L is dependent on Rac1 signaling. Rac1 controls surface mobilization of CD40L on activated platelets and MMP-9 secretion from neutrophils. Thus, our findings indicate that targeting Rac1 signaling might be a

  5. Role for CD40L in the Therapy of Human Cancer

    Institute of Scientific and Technical Information of China (English)

    Feng Wei; Xiubao Ren; Xishan Hao


    CD40L-CD40 interaction is central to the control of thymusdependent humoral .immunity and cell mediated immune responses.CD40, a member of the tumor necrosis factor receptor (TNF- R) family,has been found on the surface of B lymphocytes, monocytes, hematopoietic progenitors, dendritic cells (DCs), endothelial cells, epithelial cells and so on. Its natural ligand (CD40 ligand, CD40L), CD154, a member of the tumor necrosis factor (TNF) family, is mainly expressed on activated CD4+ T lymphocytes. A direct growth-inhibitory effect can be found when ligated CD40 is on human breast, ovarian, cervical, bladder, non-small cell lung, and squamous epithelial carcinoma cells. This effect is related to the induction of cell cycle blockage and/or apoptosis. CD40L induces phenotypic and functional maturation of DCs, and can increase tumor immunogenicity through up-regulation of costimulatory molecular expression and cytokine production by epithelial cancer cells. As a result,CD40L can enhance tumor rejection immune responses. Furthermore, by means of a "bystander effect", even CD40-negative tumor subsets can be eliminated by activated tumor-reactive cytotoxic T lymphocytes(CTL),This review summarizes recent findings on CD40L recombinant protein and gene therapy-based tumor treatment approaches.

  6. Evaluation of CD40, its ligand CD40L and Bcl-2 in psoriatic patients

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    Bożena Chodynicka


    Full Text Available Psoriasis is a chronic, recurrent, inflammatory disease. Recent investigations indicate an autoimmune pathogenesis of the disease. Apoptosis plays an important role in the regulation of immune mechanisms in many autoimmune diseases. Although CD40, CD40L, and Bcl-2 have already been studied in psoriatic skin lesions, little is known about their circulating forms. The aim of the present study was to evaluate the serum concentrations of Bcl-2, soluble CD40 and CD40L in psoriatic patients. The study was performed using ELISA kits in 39 psoriatic patients before treatment and after two weeks of topical ointment. Data was analyzed with respect to severity of psoriasis, duration of the disease, and coexisting psoriatic arthritis. Our results revealed that serum concentrations of soluble CD40 and CD40L before and after treatment were significantly higher (p < 0.01 and p < 0.001 in patients with psoriasis compared to the control group. Topical treatment of psoriatic lesions with dithranol ointment failed to decrease serum of CD40 and CD40L, which has not been described until now. There was no significant difference in serum Bcl-2 concentration between the compared groups. We did not find significant differences in serum concentrations of Bcl-2, CD40 or CD40L between patients with mild or severe psoriasis, nor any correlation between disease duration and the presence of psoriatic arthritis symptoms. Our data indicates upregulation of the CD40/CD40L system in psoriatic patients despite topical treatment and suggests their possible role in the pathogenesis of psoriasis.

  7. CD40L Deficiency Ameliorates Adipose Tissue Inflammation and Metabolic Manifestations of Obesity in Mice

    NARCIS (Netherlands)

    M. Poggi; D. Engel; A. Christ; L. Beckers; E. Wijnands; L. Boon; A. Driessen; J. Cleutjens; C. Weber; N. Gerdes; E. Lutgens


    Obese adipose tissue shows hallmarks of chronic inflammation, which promotes the development of metabolic disorders. The mechanisms by which immune cells interact with each other or with metabolism-associated cell types, and the players involved, are still unclear. The CD40-CD40L costimulatory dyad

  8. Soluble CD40L in children and adolescents with type 1 diabetes: relation to microvascular complications and glycemic control. (United States)

    El-Asrar, Mohamed A; Adly, Amira Am; Ismail, Eman A


    CD40-soluble CD40 ligand (sCD40L) interactions might constitute an important mediator for vascular inflammation that initiates diabetic microangiopathy. Little is known about the relation between sCD40L and glycemic control. Therefore, this study aimed to evaluate sCD40L levels in patients with type 1 diabetes and its relation to microvascular complications and metabolic control. Sixty patients with type 1 diabetes were compared with 30 healthy control subjects. Detailed medical history, thorough clinical examination, and laboratory assessment of high-sensitivity C-reactive protein, glycemic control, and the presence of microvascular complications were performed. Measurement of serum sCD40L levels was done using enzyme-linked immunosorbent assay. Patients were divided into two groups according to the presence of microvascular complications. Serum sCD40L levels were significantly elevated in patients with type 1 diabetes in both groups compared with healthy controls (p < 0.001). Patients with microvascular complications had higher serum sCD40L concentrations than non-complicated cases (median, 13 000 vs. 450 pg/mL; p < 0.001). Serum sCD40L cutoff value of 530 pg/mL was able to differentiate complicated from non-complicated cases (p < 0.001). Patients with microalbuminuria or peripheral neuropathy showed higher levels of sCD40L when compared with patients without these complications (p < 0.05). Serum sCD40L levels were positively correlated with hemoglobin A1c and urinary albumin excretion (p < 0.001). We suggest that serum sCD40L levels are elevated in type 1 diabetes, particularly in patients with microvascular complications and a significant correlation with glycemic control exists. Therefore, measurement of serum sCD40L levels in poorly controlled patients would help to identify those at high risk of developing microvascular complications.

  9. Human CD40L gene maps between DXS144E and DXS300 in Xq26

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    Pilia, G.; Porta, G.; Schlessinger, D. [Washington Univ., St. Louis, MO (United States)] [and others


    PCR primers for the 3{prime} end of the CD40L gene, were used to screen the YACs in the Xq26 contig. The primers were 5{prime} ACA GTC TCA CCT TGC AGG CTG and 5{prime} CTC TCT GGA TGT CTG CAT CAG. PCR amplification was for 35 cycles at 95{degree}C for 30 s, 55{degree}C for 45 s, and 72{degree}C for 45 s.

  10. Persistence of high CD40 and CD40L expression after restorative proctocolectomy for ulcerative colitis

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    Lino Polese; Mauro Frego; Davide F D'Amico; Tmerio Angriman; Giuseppe De Franchis; Attilio Cecchetto; Giacomo C. Sturniolo; Renata D'Incà; Marco Scarpa; Cesare Ruffolo; Lorenzo Norberto


    AIM: To focus on the role of CD40 and CD40L in their pathogenesis.METHODS: We analyzed by immunohistochemistry the CD40 and CD40L expression in the pouch mucosa of 28 patients who had undergone RPC for UC, in the terminal ileum of 6 patients with UC and 11 healthy subjects. We also examined by flow cytometry the expression of CD40 by B lymphocytes and monocytes in the peripheral blood of 20 pouch patients, 15 UC patients and 11 healthy controls.RESULTS: Ileal pouch mucosa leukocytes presented a significantly higher expression of CD40 and CD40L as compared to controls. This alteration correlated with pouchitis, but was also present in the healthy pouch and in the terminal ileum of UC patients. CD40 expression of peripheral B lymphocytes was significantly higher in patients with UC and pouch, respect to controls. Increased CD40 levels in blood B cells of pouch patients correlatedwith the presence of spondyloarthropathy, but not with pouchitis, or inflammatory indices.CONCLUSION: High CD40 expression in the ileal pouch mucosa could be implied in the pathogenesis of pouchitis following proctocolectomy for UC, whereas its increased levels on peripheral blood B lymphocytes are associated with the presence of extraintestinal manifestations.

  11. Immune response is an important aspect of the antitumor effect produced by a CD40L-encoding oncolytic adenovirus. (United States)

    Diaconu, Iulia; Cerullo, Vincenzo; Hirvinen, Mari L M; Escutenaire, Sophie; Ugolini, Matteo; Pesonen, Saila K; Bramante, Simona; Parviainen, Suvi; Kanerva, Anna; Loskog, Angelica S I; Eliopoulos, Aristides G; Pesonen, Sari; Hemminki, Akseli


    Oncolytic adenovirus is an attractive platform for immunotherapy because virus replication is highly immunogenic and not subject to tolerance. Although oncolysis releases tumor epitopes and provides costimulatory danger signals, arming the virus with immunostimulatory molecules can further improve efficacy. CD40 ligand (CD40L, CD154) induces apoptosis of tumor cells and triggers several immune mechanisms, including a T-helper type 1 (T(H)1) response, which leads to activation of cytotoxic T cells and reduction of immunosuppression. In this study, we constructed a novel oncolytic adenovirus, Ad5/3-hTERT-E1A-hCD40L, which features a chimeric Ad5/3 capsid for enhanced tumor transduction, a human telomerase reverse transcriptase (hTERT) promoter for tumor selectivity, and human CD40L for increased efficacy. Ad5/3-hTERT-E1A-hCD40L significantly inhibited tumor growth in vivo via oncolytic and apoptotic effects, and (Ad5/3-hTERT-E1A-hCD40L)-mediated oncolysis resulted in enhanced calreticulin exposure and HMGB1 and ATP release, which were suggestive of immunogenicity. In two syngeneic mouse models, murine CD40L induced recruitment and activation of antigen-presenting cells, leading to increased interleukin-12 production in splenocytes. This effect was associated with induction of the T(H)1 cytokines IFN-γ, RANTES, and TNF-α. Tumors treated with Ad5/3-CMV-mCD40L also displayed an enhanced presence of macrophages and cytotoxic CD8(+) T cells but not B cells. Together, our findings show that adenoviruses coding for CD40L mediate multiple antitumor effects including oncolysis, apoptosis, induction of T-cell responses, and upregulation of T(H)1 cytokines.

  12. Preliminary evidence for a matrix metalloproteinase-2 (MMP-2)-dependent shedding of soluble CD40 ligand (sCD40L) from activated platelets. (United States)

    Reinboldt, Stephan; Wenzel, Folker; Rauch, Bernhard H; Hohlfeld, Thomas; Grandoch, Maria; Fischer, Jens W; Weber, Artur-Aron


    Platelets are the major source of soluble CD40 ligand (sCD40L) in the blood. It has been demonstrated that CD40L is cleaved from the surface of activated platelets to release sCD40L. However, the enzyme involved in sCD40L shedding has not been identified yet. Using a panel of pharmacological inhibitors of serine, cysteine, aspartate, or metalloproteinases, preliminary evidence is presented for the hypothesis that matrix metalloproteinase-2 (MMP-2) might be the protease, primarily responsible for CD40L cleavage from platelet surface.

  13. Genetic adjuvantation of recombinant MVA with CD40L potentiates CD8 T cell mediated immunity

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    Henning eLauterbach


    Full Text Available Modified vaccinia Ankara (MVA is a safe and promising viral vaccine vector that is currently investigated in several clinical and pre-clinical trials. In contrast to inactivated or sub-unit vaccines, MVA is able to induce strong humoral as well as cellular immune responses. In order to further improve its CD8 T cell inducing capacity, we genetically adjuvanted MVA with the coding sequence of murine CD40L, a member of the tumor necrosis factor (TNF superfamily. Immunization of mice with this new vector led to strongly enhanced primary and memory CD8 T cell responses. Concordant with the enhanced CD8 T cell response, we could detect stronger activation of dendritic cells and higher systemic levels of innate cytokines (including IL-12p70 early after immunization. Interestingly, acquisition of memory characteristics (i.e., IL-7R expression was accelerated after immunization with MVA-CD40L in comparison to non-adjuvanted MVA. Furthermore, the generated CTLs also showed improved functionality as demonstrated by intracellular cytokine staining and in vivo killing activity. Importantly, the superior CTL response after a single MVA-CD40L immunization was able to protect B cell deficient mice against a fatal infection with ectromelia virus. Taken together, we show that genetic adjuvantation of MVA can change strength, quality and functionality of innate and adaptive immune responses. These data should facilitate a rational vaccine design with a focus on rapid induction of large numbers of CD8 T cells able to protect against specific diseases.

  14. Expression of CD40 and CD40L in Gastric Cancer Tissue and Its Clinical Significance

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    Rui Li


    Full Text Available To study expression of CD40 and CD40L in gastric cancer tissue we assessed gastric cancer patients admitted to the Department of Gastroenterology of The First Affiliated Hospital of Soochow University and control subjects. Gastric cancer and normal (from around tumours tissue samples were obtained from patients. Venous blood samples (gastric cancer and ulcer groups were drawn on the morning of the day before surgery for the measurement of peripheral sCD40L. The expression of CD40 in gastric carcinoma specimens was examined immuno-histochemically. The clinicopathological factors, including age, sex, tumor size, gross appearance, degree of cellular differentiation, histological classification, depth of tumor invasion, lymph node metastasis, peritoneal dissemination, and TNM stage were analyzed according to the different expression of CD40. The results indicated a high CD40 expression in gastric cancer tissues. This positive expression of CD40 revealed a significant (P < 0.05 correlation with lymphatic metastasis and tumor TNM stage in gastric cancer patients. It is concluded that higher CD40 expression existed in expanding type tumors and could play an important role in clinical diagnosis of gastric cancer patients.

  15. New Steroidal Glycosides Isolated as CD40L Inhibitors of Activated Platelets

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    Haifeng Chen


    Full Text Available Three new compounds were isolated from the dried bulbs of Allium macrostemon Bunge. Their structures were elucidated from their spectral data as (25R-26-O-β-D-glucopyranosyl-5α-furostane-3β,12β,22,26-tetraol-3-O-β-D-glucopyranos-yl (1→2 [β-D-glucopyranosyl (1→3]-β-D-glucopyranosyl (1→4-β-D-galactopyranoside (1, (25R-26-O-β-D-glucopyranosyl-5α-furostane-3β,12α,22,26-tetraol-3-O-β-D-glucopyranosyl (1→2 [β-D-glucopyranosyl (1→3]-β-D-glucopyranosyl (1→4-β-D-galacto- pyranoside (2 and (25R-26-O-β-D-glucopyranosyl-5β-furostane-3β,12α,22,26-tetraol-3-O-β-D-glucopyranosyl (1→2-β-D-galactopyranoside (3, respectively. The inhibition effect of all compounds on CD40 ligand (CD40L expression on the membrane of activated platelets stimulated by ADP was tested. Compounds 1 and 2 exhibited significant inhibitory activities in a dose dependent manner (P < 0.05, suggesting their potential application as CD40L inhibitors.

  16. Simvastatin antagonizes CD40L secretion, CXC chemokine formation, and pulmonary infiltration of neutrophils in abdominal sepsis. (United States)

    Zhang, Su; Rahman, Milladur; Zhang, Songen; Qi, Zhongquan; Thorlacius, Henrik


    Statins have been reported to exert anti-inflammatory actions and protect against septic organ dysfunction. Herein, we hypothesized that simvastatin may attenuate neutrophil activation and lung damage in abdominal sepsis. Male C57BL/6 mice were pretreated with simvastatin (0.5 or 10 mg/kg) before CLP. In separate groups, mice received an anti-CD40L antibody or a CXCR2 antagonist (SB225002) prior to CLP. BALF and lung tissue were harvested for analysis of neutrophil infiltration, as well as edema and CXC chemokine formation. Blood was collected for analysis of Mac-1 and CD40L expression on neutrophils and platelets, as well as soluble CD40L in plasma. Simvastatin decreased CLP-induced neutrophil infiltration and edema formation in the lung. Moreover, Mac-1 expression increased on septic neutrophils, which was significantly attenuated by simvastatin. Inhibition of CD40L reduced CLP-induced up-regulation of Mac-1 on neutrophils. Simvastatin prevented CD40L shedding from the surface of platelets and reduced circulating levels of CD40L in septic mice. CXC chemokine-induced migration of neutrophils in vitro was decreased greatly by simvastatin. Moreover, simvastatin abolished CLP-evoked formation of CXC chemokines in the lung, and a CXCR2 antagonist attenuated pulmonary accumulation of neutrophils. Our data suggest that the inhibitory effect of simvastatin on pulmonary accumulation of neutrophils may be related to a reduction of CD40L secretion into the circulation, as well as a decrease in CXC chemokine formation in the lung. Thus, these protective mechanisms help to explain the beneficial actions exerted by statins, such as simvastatin, in sepsis.

  17. Nanovesicle-targeted Kv1.3 knockdown in memory T cells suppresses CD40L expression and memory phenotype. (United States)

    Chimote, Ameet A; Hajdu, Peter; Kottyan, Leah C; Harley, John B; Yun, Yeoheung; Conforti, Laura


    Ca(2+) signaling controls activation and effector functions of T lymphocytes. Ca(2+) levels also regulate NFAT activation and CD40 ligand (CD40L) expression in T cells. CD40L in activated memory T cells binds to its cognate receptor, CD40, on other cell types resulting in the production of antibodies and pro-inflammatory mediators. The CD40L/CD40 interaction is implicated in the pathogenesis of autoimmune disorders and CD40L is widely recognized as a therapeutic target. Ca(2+) signaling in T cells is regulated by Kv1.3 channels. We have developed lipid nanoparticles that deliver Kv1.3 siRNAs (Kv1.3-NPs) selectively to CD45RO(+) memory T cells and reduce the activation-induced Ca(2+) influx. Herein we report that Kv1.3-NPs reduced NFAT activation and CD40L expression exclusively in CD45RO(+) T cells. Furthermore, Kv1.3-NPs suppressed cytokine release and induced a phenotype switch of T cells from predominantly memory to naïve. These findings indicate that Kv1.3-NPs operate as targeted immune suppressive agents with promising therapeutic potentials.

  18. CD40L induces multidrug resistance to apoptosis in breast carcinoma and lymphoma cells through caspase independent and dependent pathways

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    Blay Jean-Yves


    Full Text Available Abstract Background CD40L was found to reduce doxorubicin-induced apoptosis in non Hodgkin's lymphoma cell lines through caspase-3 dependent mechanism. Whether this represents a general mechanism for other tumor types is unknown. Methods The resistance induced by CD40L against apoptosis induced by a panel of cytotoxic chemotherapeutic drugs in non Hodgkin's lymphoma and breast carcinoma cell lines was investigated. Results Doxorubicin, cisplatyl, etoposide, vinblastin and paclitaxel increased apoptosis in a dose-dependent manner in breast carcinoma as well as in non Hodgkin's lymphoma cell lines. Co-culture with irradiated L cells expressing CD40L significantly reduced the percentage of apoptotic cells in breast carcinoma and non Hodgkin's lymphoma cell lines treated with these drugs. In breast carcinoma cell lines, these 5 drugs induced an inconsistent increase of caspase-3/7 activity, while in non Hodgkin's lymphoma cell lines all 5 drugs increased caspase-3/7 activity up to 28-fold above baseline. Co-culture with CD40L L cells reduced (-39% to -89% the activation of caspase-3/7 induced by these agents in all 5 non Hodgkin's lymphoma cell lines, but in none of the 2 breast carcinoma cell lines. Co culture with CD40L L cells also blocked the apoptosis induced by exogenous ceramides in breast carcinoma and non Hodgkin's lymphoma cell lines through a caspase-3-like, 8-like and 9-like dependent pathways. Conclusion These results indicate that CD40L expressed on adjacent non tumoral cells induces multidrug resistance to cytotoxic agents and ceramides in both breast carcinoma and non Hodgkin's lymphoma cell lines, albeit through a caspase independent and dependent pathway respectively.

  19. Excess soluble CD40L contributes to blood brain barrier permeability in vivo: implications for HIV-associated neurocognitive disorders.

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    Donna C Davidson

    Full Text Available Despite the use of anti-retroviral therapies, a majority of HIV-infected individuals still develop HIV-Associated Neurocognitive Disorders (HAND, indicating that host inflammatory mediators, in addition to viral proteins, may be contributing to these disorders. Consistently, we have previously shown that levels of the inflammatory mediator soluble CD40L (sCD40L are elevated in the circulation of HIV-infected, cognitively impaired individuals as compared to their infected, non-impaired counterparts. Recent studies from our group suggest a role for the CD40/CD40L dyad in blood brain barrier (BBB permeability and interestingly, sCD40L is thought to regulate BBB permeability in other inflammatory disorders of the CNS. Using complementary multiphoton microscopy and quantitative analyses in wild-type and CD40L deficient mice, we now reveal that the HIV transactivator of transcription (Tat can induce BBB permeability in a CD40L-dependent manner. This permeability of the BBB was found to be the result of aberrant platelet activation induced by Tat, since depletion of platelets prior to treatment reversed Tat-induced BBB permeability. Furthermore, Tat treatment led to an increase in granulocyte antigen 1 (Gr1 positive monocytes, indicating an expansion of the inflammatory subset of cells in these mice, which were found to adhere more readily to the brain microvasculature in Tat treated animals. Exploring the mechanisms by which the BBB becomes compromised during HIV infection has the potential to reveal novel therapeutic targets, thereby aiding in the development of adjunct therapies for the management of HAND, which are currently lacking.

  20. Excess soluble CD40L contributes to blood brain barrier permeability in vivo: implications for HIV-associated neurocognitive disorders. (United States)

    Davidson, Donna C; Hirschman, Michael P; Sun, Anita; Singh, Meera V; Kasischke, Karl; Maggirwar, Sanjay B


    Despite the use of anti-retroviral therapies, a majority of HIV-infected individuals still develop HIV-Associated Neurocognitive Disorders (HAND), indicating that host inflammatory mediators, in addition to viral proteins, may be contributing to these disorders. Consistently, we have previously shown that levels of the inflammatory mediator soluble CD40L (sCD40L) are elevated in the circulation of HIV-infected, cognitively impaired individuals as compared to their infected, non-impaired counterparts. Recent studies from our group suggest a role for the CD40/CD40L dyad in blood brain barrier (BBB) permeability and interestingly, sCD40L is thought to regulate BBB permeability in other inflammatory disorders of the CNS. Using complementary multiphoton microscopy and quantitative analyses in wild-type and CD40L deficient mice, we now reveal that the HIV transactivator of transcription (Tat) can induce BBB permeability in a CD40L-dependent manner. This permeability of the BBB was found to be the result of aberrant platelet activation induced by Tat, since depletion of platelets prior to treatment reversed Tat-induced BBB permeability. Furthermore, Tat treatment led to an increase in granulocyte antigen 1 (Gr1) positive monocytes, indicating an expansion of the inflammatory subset of cells in these mice, which were found to adhere more readily to the brain microvasculature in Tat treated animals. Exploring the mechanisms by which the BBB becomes compromised during HIV infection has the potential to reveal novel therapeutic targets, thereby aiding in the development of adjunct therapies for the management of HAND, which are currently lacking.

  1. CD40L deficiency attenuates diet-induced adipose tissue inflammation by impairing immune cell accumulation and production of pathogenic IgG-antibodies.

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    Dennis Wolf

    Full Text Available BACKGROUND: Adipose tissue inflammation fuels the metabolic syndrome. We recently reported that CD40L--an established marker and mediator of cardiovascular disease--induces inflammatory cytokine production in adipose cells in vitro. Here, we tested the hypothesis that CD40L deficiency modulates adipose tissue inflammation in vivo. METHODOLOGY/PRINCIPAL FINDINGS: WT or CD40L(-/- mice consumed a high fat diet (HFD for 20 weeks. Inflammatory cell recruitment was impaired in mice lacking CD40L as shown by a decrease of adipose tissue macrophages, B-cells, and an increase in protective T-regulatory cells. Mechanistically, CD40L-deficient mice expressed significantly lower levels of the pro-inflammatory chemokine MCP-1 both, locally in adipose tissue and systemically in plasma. Moreover, levels of pro-inflammatory IgG-antibodies against oxidized lipids were reduced in CD40L(-/- mice. Also, circulating low-density lipoproteins and insulin levels were lower in CD40L(-/- mice. However, CD40L(-/- mice consuming HFD were not protected from the onset of diet-induced obesity (DIO, insulin resistance, and hepatic steatosis, suggesting that CD40L selectively limits the inflammatory features of diet-induced obesity rather than its metabolic phenotype. Interestingly, CD40L(-/- mice consuming a low fat diet (LFD showed both, a favorable inflammatory and metabolic phenotype characterized by diminished weight gain, improved insulin tolerance, and attenuated plasma adipokine levels. CONCLUSION: We present the novel finding that CD40L deficiency limits adipose tissue inflammation in vivo. These findings identify CD40L as a potential mediator at the interface of cardiovascular and metabolic disease.

  2. PU.1 Expression in T Follicular Helper Cells Limits CD40L-Dependent Germinal Center B Cell Development. (United States)

    Awe, Olufolakemi; Hufford, Matthew M; Wu, Hao; Pham, Duy; Chang, Hua-Chen; Jabeen, Rukhsana; Dent, Alexander L; Kaplan, Mark H


    PU.1 is an ETS family transcription factor that is important for the development of multiple hematopoietic cell lineages. Previous work demonstrated a critical role for PU.1 in promoting Th9 development and in limiting Th2 cytokine production. Whether PU.1 has functions in other Th lineages is not clear. In this study, we examined the effects of ectopic expression of PU.1 in CD4(+) T cells and observed decreased expression of genes involved with the function of T follicular helper (Tfh) cells, including Il21 and Tnfsf5 (encoding CD40L). T cells from conditional mutant mice that lack expression of PU.1 in T cells (Sfpi1(lck-/-)) demonstrated increased production of CD40L and IL-21 in vitro. Following adjuvant-dependent or adjuvant-independent immunization, we observed that Sfpi1(lck-/-) mice had increased numbers of Tfh cells, increased germinal center B cells (GCB cells), and increased Ab production in vivo. This correlated with increased expression of IL-21 and CD40L in Tfh cells from Sfpi1(lck-/-) mice compared with control mice. Finally, although blockade of IL-21 did not affect GCB cells in Sfpi1(lck-/-) mice, anti-CD40L treatment of immunized Sfpi1(lck-/-) mice decreased GCB cell numbers and Ag-specific Ig concentrations. Together, these data indicate an inhibitory role for PU.1 in the function of Tfh cells, germinal centers, and Tfh-dependent humoral immunity.

  3. IL-21 and CD40L synergistically promote plasma cell differentiation through upregulation of Blimp-1 in human B cells. (United States)

    Ding, B Belinda; Bi, Enguang; Chen, Hongshan; Yu, J Jessica; Ye, B Hilda


    After undergoing Ig somatic hypermutation and Ag selection, germinal center (GC) B cells terminally differentiate into either memory or plasma cells (PCs). It is known that the CD40L and IL-21/STAT3 signaling pathways play critical roles in this process, yet it is unclear how the B cell transcription program interprets and integrates these two types of T cell-derived signals. In this study, we characterized the role of STAT3 in the GC-associated PC differentiation using purified human tonsillar GC B cells and a GC B cell-like cell line. When primary GC B cells were cultured under PC differentiation condition, STAT3 inhibition by AG490 prevented the transition from GC centrocytes to preplasmablast, suggesting that STAT3 is required for the initiation of PC development. In a GC B cell-like human B cell line, although IL-21 alone can induce low-level Blimp-1 expression, maximum Blimp-1 upregulation and optimal PC differentiation required both IL-21 and CD40L. CD40L, although having no effect on Blimp-1 as a single agent, greatly augmented the amplitude and duration of IL-21-triggered Jak-STAT3 signaling. In the human PRDM1 locus, CD40L treatment enhanced the ability of STAT3 to upregulate Blimp-1 by removing BCL6, a potent inhibitor of Blimp-1 expression, from a shared BCL6/STAT3 site in intron 3. Thus, IL-21 and CD40L collaborate through at least two distinct mechanisms to synergistically promote Blimp-1 activation and PC differentiation.

  4. CD40/CD40L Dyad in the Inflammatory and Immune Responses in the Central Nervous System

    Institute of Scientific and Technical Information of China (English)

    Keqiang Chen; Jian Huang; Wanghua Gong; Lingzhi Zhang; Peichu Yu; Ji Ming Wang


    CD40 and its cognate ligand (CD40L) are a pair of regulators of pro-inflammatory and immune responses. In the central nervous system (CNS), CD40 is expressed on a variety of cells, including vascular endothelial cells, smooth muscle cells, astrocytes and microglia (the brain macrophages, being the most sensitive cell type to respond to CD40 ligand). Interaction between CD40 on microglia and CD40L presented by infiltrating T lymphocytes and other resident CNS cells triggers a series of intracellular signaling events that promote the production of a wide array of cytokines, chemokines and neurotoxins. Thus, both molecules serve as amplifiers of pro-inflammatory and immune responses in the CNS and constitute important molecular targets for therapeutic intervention of diseases.

  5. Incorporation of GM-CSF or CD40L Enhances the Immunogenicity of Hantaan Virus-Like Particles

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    Lin-Feng Cheng


    Full Text Available A safe and effective Hantaan virus (HTNV vaccine is highly desirable because HTNV causes an acute and often fatal disease (hemorrhagic fever with renal syndrome, HFRS. Since the immunity of the inactivated vaccine is weak and the safety is poor, HTNV virus-like particles (VLPs offer an attractive and safe alternative. These particles lack the viral genome but are perceived by the immune system as virus particles. We hypothesized that adding immunostimulatory signals to VLPs would enhance their efficacy. To accomplish this enhancement, we generated chimeric HTNV VLPs containing glycosylphosphatidylinositol (GPI-anchored granulocyte macrophage colony-stimulating factor (GM-CSF or CD40 ligand (CD40L and investigated their biological activity in vitro. The immunization of mice with chimeric HTNV VLPs containing GM-CSF or CD40L induced stronger humoral immune responses and cellular immune responses compared to the HTNV VLPs and Chinese commercial inactivated hantavirus vaccine. Chimeric HTNV VLPs containing GM-CSF or CD40L also protected mice from an HTNV challenge. Altogether, our results suggest that anchoring immunostimulatory molecules into HTNV VLPs can be a potential approach for the control and prevention of HFRS.

  6. A GM-CSF and CD40L bystander vaccine is effective in a murine breast cancer model

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    Soliman H


    -γ secreting T-cells on ELISPOT for BCG treated groups, and a trend for higher numbers of tumor infiltrating CD3+ lymphocytes. Some tumors in the 4T1-BCG demonstrated organized lymphoid structures within the tumor microenvironment as well. Conclusion: The use of BCG bystander cell lines demonstrates proof of concept for anti-tumor activity and immunogenicity in an immunocompetent murine model of breast cancer. This vaccine is being evaluated in lung cancer and should be explored further in clinical trials of breast cancer patients at high risk of recurrence or in combination with other immunomodulatory agents. Keywords: breast cancer, immunotherapy, bystander vaccine, CD40L, GM-CSF

  7. Assessment of serum levels of soluble CD40L in Egyptian children and adolescents with type 1 diabetes mellitus: Relationship to microalbuminuria and glycemic control

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    Kotb Abbass Metwalley


    Full Text Available Context: Soluble CD40 ligand (sCD40L is known to be elevated in different clinical situations including hypercholesterolemia, acute coronary syndromes, and type 2 diabetes mellitus (T2DM, Data about the relationship between type 1 diabetes mellitus (T1DM and sCD40L is limited. In addition, the potential role ofsCD40Lin the pathogenesis of vascular complications in children and adolescents with T1DM is to be clarified. Hence, the study aimed at assessment of sCD40L levels in children and adolescents with T1DM and correlation of these levels with glycemic control and microalbuminuria. Settings and Design: Cross-sectional controlled study. Materials and Methods: The study was performed in the Pediatric Endocrinology and Diabetes Unit, Assuit University Children Hospital, Assiut, Egypt. It included 70 children and adolescents with T1DM (mean age 14. 76 ± 2.21 years. Cases were further subdivided into 43 cases with normoalbuminuria and 27 cases with microalbuminuria according to presence or absence or microalbuminuria in fresh urine samples. Twentyfive healthy subjects, age- and sex-matched were included as control group (mean age = 13.62 ± 2.11 years. Studied cases were subjected to medical history, clinical examination, and laboratory assessment of fasting blood glucose (FBG, lipid profile, glycosylated hemoglobin (HbA1c, and sCD40L were performed. Results: Mean HbA1c and sCD40L were significantly higher in diabetic children (n = 70 compared to control (n = 25 (P < 0.001 for each. Mean HbA1c and sCD40L levels were significantly higher in microalbuminuric cases (n = 27 compared to normoalbuminuric cases (n = 43 (P < 0.05 and <0.01, respectively.We also observed a significant positive correlation between sCD40L levels and the age, diabetes duration, HbA1c, and urinary albumin creatinine ratio. Conclusions: The high serum sCD40L levels in children and adolescents with T1DM particularly in those with microalbminuria and its positive correlation with

  8. Protective Mechanisms of Guanosine from Solanum lycopersicum on Agonist-Induced Platelet Activation: Role of sCD40L

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    Iván Palomo


    Full Text Available In the past 30 years, only three natural products have been sources of new drugs with antiplatelet activity. In this study, we have demonstrated for the first time that guanosine from Solanum lycopersicum possesses antiplatelet (secretion, spreading, adhesion and aggregation activity in vitro and inhibition of platelet inflammatory mediator of atherosclerosis (sCD40L. According to ADP-induced platelet aggregation inhibiting, the total extract residue was fractionated by liquid chromatography/phase separation, affording an aqueous fraction. This fraction was subjected to repeated permeation over Sephadex LH-20 and semi-preparative TLC. The isolated compound finally obtained was identified as guanosine on the basis of its UV-spectra, HPLC and 1H-NMR data. Guanosine concentration dose-dependently (1 to 4 mmol/L inhibited platelet secretion and aggregation induced by ADP and collagen. Spread of human platelets on collagen in the presence of guanosine was fully inhibited. After incubation of whole blood with guanosine, the platelet adhesion and aggregation under flow conditions was inhibited concentration dependently (0.2 to 2 mmol/L. At the same concentrations that guanosine inhibits platelet aggregation, levels of sCD40L were significantly decreased. Guanosine is thus likely to exert significant protective effects in thromboembolic-related disorders by inhibiting platelet aggregation.

  9. The involvement of the CD40-CD40L pathway in activated platelet-induced changes in HUVEC COX-2 and PPARα expression. (United States)

    Wu, Yan-qing; Chen, Xiao-shu; Chai, Jun-bing


    We aim to determine the extent of the CD40-CD40L pathway involvement in activated platelet-induced changes in human umbilical endothelial cells (HUVECs). Activated platelets were co-incubated with HUVECs in the presence or absence of CD40LmAb. HUVECs were also directly stimulated with rhCD40L. HUVEC endothelial cyclooxygenase 2 (COX-2) and peroxisome proliferator-activated receptor alpha (PPARα) expression was then assessed. To estimate COX-2 activity, PGE2 concentration was determined. PPARα activity was assessed using a nuclear factor activity kit. Co-incubation with activated platelets increased HUVEC COX-2 and PPARα mRNA expression (P HUVEC COX-2 mRNA and protein (P HUVEC COX-2 expression and activity partly through the CD40-CD40L pathway.

  10. Dendritic cells induce Tc1 cell differentiation via the CD40/CD40L pathway in mice after exposure to cigarette smoke. (United States)

    Kuang, Liang-Jian; Deng, Ting-Ting; Wang, Qin; Qiu, Shi-Lin; Liang, Yi; He, Zhi-Yi; Zhang, Jian-Quan; Bai, Jing; Li, Mei-Hua; Deng, Jing-Min; Liu, Guang-Nan; Liu, Ji-Feng; Zhong, Xiao-Ning


    Dendritic cells and CD8(+) T cells participate in the pathology of chronic obstructive pulmonary disease, including emphysema, but little is known of the involvement of the CD40/CD40L pathway. We investigated the role of the CD40/CD40L pathway in Tc1 cell differentiation induced by dendritic cells in a mouse model of emphysema, and in vitro. C57BL/6J wild-type and CD40(-/-) mice were exposed to cigarette smoke (CS) or not (control), for 24 wk. In vitro experiments involved wild-type and CD40(-/-) dendritic cells treated with CS extract (CSE) or not. Compared with the control groups, the CS mice (both wild type and CD40(-/-)) had a greater percentage of lung dendritic cells and higher levels of major histocompatability complex (MHC) class I molecules and costimulatory molecules CD40 and CD80. Relative to the CS CD40(-/-) mice, the CS wild type showed greater signs of lung damage and Tc1 cell differentiation. In vitro, the CSE-treated wild-type cells evidenced more cytokine release (IL-12/p70) and Tc1 cell differentiation than did the CSE-treated CD40(-/-) cells. Exposure to cigarette smoke increases the percentage of lung dendritic cells and promotes Tc1 cell differentiation via the CD40/CD40L pathway. Blocking the CD40/CD40L pathway may suppress development of emphysema in mice exposed to cigarette smoke.

  11. Constitutive CD40L expression on B cells prematurely terminates germinal center response and leads to augmented plasma cell production in T cell areas. (United States)

    Bolduc, Anna; Long, Eugene; Stapler, Dale; Cascalho, Marilia; Tsubata, Takeshi; Koni, Pandelakis A; Shimoda, Michiko


    CD40/CD40L engagement is essential to T cell-dependent B cell proliferation and differentiation. However, the precise role of CD40 signaling through cognate T-B interaction in the generation of germinal center and memory B cells is still incompletely understood. To address this issue, a B cell-specific CD40L transgene (CD40LBTg) was introduced into mice with B cell-restricted MHC class II deficiency. Using this mouse model, we show that constitutive CD40L expression on B cells alone could not induce germinal center differentiation of MHC class II-deficient B cells after immunization with T cell-dependent Ag. Thus, some other MHC class II-dependent T cell-derived signals are essential for the generation of germinal center B cells in response to T cell-dependent Ag. In fact, CD40LBTg mice generated a complex Ag-specific IgG1 response, which was greatly enhanced in early, but reduced in late, primary response compared with control mice. We also found that the frequency of Ag-specific germinal center B cells in CD40LBTg mice was abruptly reduced 1 wk after immunization. As a result, the numbers of Ag-specific IgG1 long-lived plasma cells and memory B cells were reduced. By histology, large numbers of Ag-specific plasma cells were found in T cell areas adjacent to Ag-specific germinal centers of CD40LBTg mice, temporarily during the second week of primary response. These results indicate that CD40L expression on B cells prematurely terminated their ongoing germinal center response and produced plasma cells. Our results support the notion that CD40 signaling is an active termination signal for germinal center reaction.

  12. Earlier low-dose TBI or DST overcomes CD8+ T-cell-mediated alloresistance to allogeneic marrow in recipients of anti-CD40L. (United States)

    Takeuchi, Yasuo; Ito, Hiroshi; Kurtz, Josef; Wekerle, Thomas; Ho, Leon; Sykes, Megan


    Treatment with a single injection of anti-CD40L (CD154) monoclonal antibody (mAb) and fully mismatched allogeneic bone marrow transplant (BMT) allows rapid tolerization of CD4+ T cells to the donor. The addition of in vivo CD8 T-cell depletion leads to permanent mixed hematopoietic chimerism and tolerance. We now describe two approaches that obviate the requirement for CD8 T-cell depletion by rapidly tolerizing recipient CD8 T cells in addition to CD4 cells. Administration of donor-specific transfusion (DST) to mice receiving 3 Gy total body irradiation (TBI), BMT and anti-CD40L mAb on day 0 uniformly led to permanent mixed chimerism and tolerance, compared with only 40% of mice receiving similar treatment without DST. In the absence of DST, moving the timing of 3 Gy TBI to day -1 or day -2 instead of day 0 led to rapid (by 2 weeks) induction of CD8+ cell tolerance, and also permitted uniform achievement of permanent mixed chimerism and donor-specific tolerance in recipients of anti-CD40L and BMT on day 0. These nontoxic regimens overcome CD8+ and CD4+ T-cell-mediated alloresistance without requiring host T-cell depletion, permitting the induction of permanent mixed chimerism and tolerance.

  13. B-cell activation with CD40L or CpG measures the function of B-cell subsets and identifies specific defects in immunodeficient patients. (United States)

    Marasco, Emiliano; Farroni, Chiara; Cascioli, Simona; Marcellini, Valentina; Scarsella, Marco; Giorda, Ezio; Piano Mortari, Eva; Leonardi, Lucia; Scarselli, Alessia; Valentini, Diletta; Cancrini, Caterina; Duse, Marzia; Grimsholm, Ola; Carsetti, Rita


    Around 65% of primary immunodeficiencies are antibody deficiencies. Functional tests are useful tools to study B-cell functions in vitro. However, no accepted guidelines for performing and evaluating functional tests have been issued yet. Here, we report our experience on the study of B-cell functions in infancy and throughout childhood. We show that T-independent stimulation with CpG measures proliferation and differentiation potential of memory B cells. Switched memory B cells respond better than IgM memory B cells. On the other hand, CD40L, a T-dependent stimulus, does not induce plasma cell differentiation, but causes proliferation of naïve and memory B cells. During childhood, the production of plasmablasts in response to CpG increases with age mirroring the development of memory B cells. The response to CD40L does not change with age. In patients with selective IgA deficiency (SIgAD), we observed that switched memory B cells are reduced due to the absence of IgA memory B cells. In agreement, IgA plasma cells are not generated in response to CpG. Unexpectedly, B cells from SIgAD patients show a reduced proliferative response to CD40L. Our results demonstrate that functional tests are an important tool to assess the functions of the humoral immune system.

  14. IL-21 and CD40L synergistically promote plasma cell differentiation through upregulation of Blimp-1 in human B cells1


    Ding, B. Belinda; Bi, Enguang; Chen, Hongshan; Yu, J. Jessica; Ye, B. Hilda


    After undergoing Ig somatic hypermutation and antigen selection, germinal center (GC) B cells terminally differentiate into either memory or plasma cells (PCs). It is known that the CD40L and IL-21/STAT3 signaling pathways play critical roles in this process, yet it is unclear how the B cell transcription program interprets and integrates these two types of T cell derived signals. In this study, we characterized the role of STAT3 in the GC-associated PC differentiation using purified human to...

  15. Effect of Simvastatin and Metformin on Aortic Configurational Changes and CD40/CD40L Expression in Atherosclerosis Rats%辛伐他汀和二甲双胍对动脉粥样硬化大鼠动脉构型及CD40/CD40L表达的影响

    Institute of Scientific and Technical Information of China (English)

    黄皓章; 黄露霜; 尹明景; 朱继金


    intervention mechanism. Methods A total of 50 healthy SD male rats, aged 8 weeks, weight about 200 g,were randomly divided into 5 groups( n = 10 ):Group N ( normal control group ),Group SF( high salt + high fat group ), Group ST( high fat plus high salt + simvastatin group ), Group MT( high fat plus high salt + metformin group ),Group ST +MT( high fat plus high salt + simvastatin + metformin group ). After 16-week feeding,the rats in each group were detected for blood lipid, aortic pathology and configuration, serum sCD40L level and the expression of CD40L in arterial tissue. Results ① Blood lipid:In Group SF,total cholesterol( TC ), triglyceride( TG ) were significantly higher than those in Group N( P 0. 05 );TC,TG in Group MT and Group ST + MT were significantly lower than those in Group N( P MT > ST > ST + MT ). The ratio of lumen area/total vascular area( LA/TV A ) in Group SF was smaller than those in Group N,Group ST,Group MT,Group ST + MT( P 0. 05 ). ④ Serum sCD40L level:In Group SF.the serum concentration of sCEMOL was higher than those in Group N,Group ST,Group MT and Group ST + MT( P 0.05 ). ⑤ Expression of CD40L in arterial tissues:The expression of CD40L in Group SF was higher than those in Group N, Group ST, Group MT and Group ST + MT( P 0. 05 ). Conclusion The level of serum sCD40L and expression of CD40L in arterial tissues increase in AS rats. Both simvastatin and metformin have an anti-atherosclerosis effect by reducing blood lipid, inhibiting the expression of CD40L and relieving inflammatory response. Biguanides drugs have a more significant effect for decreasing blood lipid while statins drugs are better in protecting vessel and improving AS. The combination of the two drugs above is superior to either of them in effect.

  16. T Cell Cancer Therapy Requires CD40-CD40L Activation of Tumor Necrosis Factor and Inducible Nitric-Oxide-Synthase-Producing Dendritic Cells. (United States)

    Marigo, Ilaria; Zilio, Serena; Desantis, Giacomo; Mlecnik, Bernhard; Agnellini, Andrielly H R; Ugel, Stefano; Sasso, Maria Stella; Qualls, Joseph E; Kratochvill, Franz; Zanovello, Paola; Molon, Barbara; Ries, Carola H; Runza, Valeria; Hoves, Sabine; Bilocq, Amélie M; Bindea, Gabriela; Mazza, Emilia M C; Bicciato, Silvio; Galon, Jérôme; Murray, Peter J; Bronte, Vincenzo


    Effective cancer immunotherapy requires overcoming immunosuppressive tumor microenvironments. We found that local nitric oxide (NO) production by tumor-infiltrating myeloid cells is important for adoptively transferred CD8(+) cytotoxic T cells to destroy tumors. These myeloid cells are phenotypically similar to inducible nitric oxide synthase (NOS2)- and tumor necrosis factor (TNF)-producing dendritic cells (DC), or Tip-DCs. Depletion of immunosuppressive, colony stimulating factor 1 receptor (CSF-1R)-dependent arginase 1(+) myeloid cells enhanced NO-dependent tumor killing. Tumor elimination via NOS2 required the CD40-CD40L pathway. We also uncovered a strong correlation between survival of colorectal cancer patients and NOS2, CD40, and TNF expression in their tumors. Our results identify a network of pro-tumor factors that can be targeted to boost cancer immunotherapies.

  17. Direct Interaction of CD40 on Tumor Cells with CD40L on T Cells Increases the Proliferation of Tumor Cells by Enhancing TGF-β Production and Th17 Differentiation.

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    Hyemin Kim

    Full Text Available It has recently been reported that the CD40-CD40 ligand (CD40L interaction is important in Th17 development. In addition, transforming growth factor-beta (TGF-β promotes tumorigenesis as an immunosuppressive cytokine and is crucial in the development of Th17 cells. This study investigated the role of CD40 in breast cancer cells and its role in immunosuppressive function and tumor progression. CD40 was highly expressed in the breast cancer cell line MDA-MB231, and its stimulation with CD40 antibodies caused the up-regulation of TGF-β. Direct CD40-CD40L interaction between MDA-MB231 cells and activated T cells also increased TGF-β production and induced the production of IL-17, which accelerated the proliferation of MDA-MB231 cells through the activation of STAT3. Taken together, the direct CD40-CD40L interaction of breast tumor cells and activated T cells increases TGF-β production and the differentiation of Th17 cells, which promotes the proliferation of breast cancer cells.


    Institute of Scientific and Technical Information of China (English)

    刘磊; 潘娟娟; 凌怡; 潘力健; 龚辉


    Objective To investigate whether the consumption of coffee affects platelets function.Methods Twelve healthy men were enrolled in a 3-week crossover study. In 3 different sessions, subjects drank either coffee (containing 180 mg caffeine), or a caffeine tablet (180mg), or placebo. Platelet glycoproteins Ⅱb/Ⅲa (GPⅡb/Ⅲa), and CD40L expression were detected by flow cytometry at 0h, 2h, 4h. Effects of different concentrations of caffeine on platelet GPⅡb/Ⅲa were detected in vitro.Results Coffee drinking inhibited ADP induced GPⅡb/Ⅲa (P<0.05 VS control at 2h and 4h) and CD40L expression (P<0.05 VS control at 2h and 4h). Coffee drinking also inhibited arachidonic acid induced GPⅡb/Ⅲa (P<0.05 VS control at 2h and 4h) and CD40L expression (P<0.05 VS control at 2h). Caffeine intake did not affect platelet GPⅡb/Ⅲa, CD40L expression induced by the agonists.Conclusion These results indicate that coffee is active in inhibiting platelet GPⅡb/Ⅲa and CD40L expression to some extent in vivo, and may be responsible for the beneficial effects of platelet function. Caffeine dose not show such effect at safe concentrations.%目的 研究咖啡对血小板功能的影响,阐明其中可能的机制.方法 12名健康男性被随机分配到三组之一,进行为期3w的交叉试验,分别饮用相同咖啡因含量(180 mg)的咖啡、咖啡因片剂或安慰剂.分别在即刻0、2、4h采血,对血小板进行全血流式细胞仪分析,测定血小板活化状态糖蛋白ⅡbⅢa(glycoprotein ⅡbⅢa, GPⅡbⅢa)、CD40L表达.另在体外,测定不同浓度咖啡因对血小板GPⅡbⅢa影响.结果 与对照组比较,饮用咖啡抑制二磷酸腺苷(ADP)诱导的GPⅡbⅢa表达(2h和4h,P <0.05)和CD40L表达(2h和4h,P <0.05).咖啡也抑制花生四烯酸诱导GPⅡbⅢa表达(2h和4h,P <0.05)和CD40L表达(2h,P <0.05).安全剂量咖啡因的摄入不影响血小板活化后GPⅡbⅢa和CD40L表达.结论 咖啡在体内可以通

  19. Induction of IL-12 Production in Human Peripheral Monocytes by Trypanosoma cruzi Is Mediated by Glycosylphosphatidylinositol-Anchored Mucin-Like Glycoproteins and Potentiated by IFN-γ and CD40-CD40L Interactions

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    Lúcia Cristina Jamli Abel


    Full Text Available Chagas disease, caused by the protozoan parasite Trypanosoma cruzi (T. cruzi, is characterized by immunopathology driven by IFN-γ secreting Th1-like T cells. T. cruzi has a thick coat of mucin-like glycoproteins covering its surface, which plays an important role in parasite invasion and host immunomodulation. It has been extensively described that T. cruzi or its products—like GPI anchors isolated from GPI-anchored mucins from the trypomastigote life cycle stage (tGPI-mucins—are potent inducers of proinflammatory responses (i.e., cytokines and NO production by IFN-γ primed murine macrophages. However, little is known about whether T. cruzi or GPI-mucins exert a similar action in human cells. We therefore decided to further investigate the in vitro cytokine production profile from human mononuclear cells from uninfected donors exposed to T. cruzi as well as tGPI-mucins. We observed that both living T. cruzi trypomastigotes and tGPI-mucins are potent inducers of IL-12 by human peripheral blood monocytes and this effect depends on CD40-CD40L interaction and IFN-γ. Our findings suggest that the polarized T1-type cytokine profile seen in T. cruzi infected patients might be a long-term effect of IL-12 production induced by lifelong exposure to T. cruzi tGPI-mucins.

  20. Cell enrichment-free massive ex-vivo expansion of peripheral CD20⁺ B cells via CD40-CD40L signals in non-human primates. (United States)

    Kim, Jung-Sik; Byun, Nari; Chung, Hyunwoo; Kim, Hyun-Je; Kim, Jong-Min; Chun, Taehoon; Lee, Won-Woo; Park, Chung-Gyu


    Non-human primates (NHPs) are valuable as preclinical resources that bridge the gap between basic science and clinical application. B cells from NHPs have been utilized for the development of B-cell targeted drugs and cell-based therapeutic modalities; however, few studies on the ex-vivo expansion of monkey B cells have been reported. In this study, we developed a highly efficient ex-vivo expansion protocol for monkey B cells resulting in 99% purity without the requirement for prior cell-enrichment procedures. To this end, monkey peripheral blood mononuclear cells (PBMCs) were stimulated for 12 days with cells constitutively expressing monkey CD40L in expansion medium optimized for specific and massive expansion of B cells. The B cells expansion rates obtained were 2-5 times higher than those previously reported in humans, with rates ranging from 7.9 to 16.6 fold increase. Moreover, expanded B cells sustained high expression of co-stimulatory molecules including CD83 and CD86 until day 12 of culture, and the simple application of a brief centrifugation resulted in a CD20(+) B cell purity rate of greater than 99%. Furthermore, small amounts of CD3(+)CD20(+)BT-like cells were generated and CD16 was expressed at moderate levels on expanded B cells. Thus, the establishment of this protocol provides a method to produce quantities of homogeneous, mature B cells in numbers sufficient for the in vitro study of B cell immunity as well as for the development of B cell-diagnostic tools and cell-based therapeutic modalities.

  1. Th cells promote CTL survival and memory via acquired pMHC-I and endogenous IL-2 and CD40L signaling and by modulating apoptosis-controlling pathways.

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    Channakeshava Sokke Umeshappa

    Full Text Available Involvement of CD4(+ helper T (Th cells is crucial for CD8(+ cytotoxic T lymphocyte (CTL-mediated immunity. However, CD4(+ Th's signals that govern CTL survival and functional memory are still not completely understood. In this study, we assessed the role of CD4(+ Th cells with acquired antigen-presenting machineries in determining CTL fates. We utilized an adoptive co-transfer into CD4(+ T cell-sufficient or -deficient mice of OTI CTLs and OTII Th cells or Th cells with various gene deficiencies pre-stimulated in vitro by ovalbumin (OVA-pulsed dendritic cell (DCova. CTL survival was kinetically assessed in these mice using FITC-anti-CD8 and PE-H-2K(b/OVA257-264 tetramer staining by flow cytometry. We show that by acting via endogenous CD40L and IL-2, and acquired peptide-MHC-I (pMHC-I complex signaling, CD4(+ Th cells enhance survival of transferred effector CTLs and their differentiation into the functional memory CTLs capable of protecting against highly-metastasizing tumor challenge. Moreover, RT-PCR, flow cytometry and Western blot analysis demonstrate that increased survival of CD4(+ Th cell-helped CTLs is matched with enhanced Akt1/NF-κB activation, down-regulation of TRAIL, and altered expression profiles with up-regulation of prosurvival (Bcl-2 and down-regulation of proapoptotic (Bcl-10, Casp-3, Casp-4, Casp-7 molecules. Taken together, our results reveal a previously unexplored mechanistic role for CD4(+ Th cells in programming CTL survival and memory recall responses. This knowledge could also aid in the development of efficient adoptive CTL cancer therapy.

  2. 血清sCD40L、脂联素水平与2型糖尿病并发急性冠脉综合征的关系及其临床意义%Correlations of serum sCD40L,adiponectin level and type 2 diabetic acute coronary Syndrome complication and its clinical significance

    Institute of Scientific and Technical Information of China (English)

    彭紫元; 张琼丽; 丘创华; 李卓成


    Objective:To explore the relation between serum sCD40L、adiponectin level and type2 diabetic acute coronary Syndrome complication and its clinical significance.Methods: Serum levels of sCD40L and adiponectin were measured with ELISA in 62 cases of type 2 diabetic patients with ACS complications, 61 cases of the absence of no complications in patients with type 2 diabetes and 60 healthy subjects as controls.Results: The levels of serum sCD40L and FPG in type 2 diabetic patients with ACS group and no complications group were higher than that of control group respectively ( all P< 0.01 ), while the adiponectin was significantly lower.The levels of serum sCD40L in type 2 diabetic patients with ACS group was higher than that of in no complications group, and the adiponectin was also lower.The levels of serum sCD40L in type 2 diabetic patients with UA group was higher than that of in type 2 diabetic patients with AMI group, while the adiponectin was converse.The serum level of sCD40L is significantly negative correlation with adiponectin ( r = - 0.765, P < 0.01 ), and there were no correlation between the serum level of FPG and sCD40L, adiponectin( r = 0.076, r = -0.11 6, all P > 0.05 ).Conclusion: Serum sCD40L and adiponectin may be involved in the pathogenesis of 2 diabetic patients with ACS,which may be a predictor of 2 diabetic patients with ACS complications.%目的:探讨血清可溶性细胞表面分化抗原CD40配体(sCD40L)、脂联素水平与2型糖尿病并发急性冠脉综合征的关系及其临床意义.方法:采用ELISA检测62例2型糖尿病并发急性冠脉综合征患者、61例无并发症的2型糖尿病患者血清sCD40L和脂联素浓度,并以60例健康人作为对照.结果:2型糖尿病并发ACS组的血清sCD40L和FPG水平高于无并发症组及正常对照组(均P0.05).结论:血清sCD40L、APN可能参与了2型糖尿病并发ACS的发病过程,可能成为ACS并发症的预测因子.

  3. 丹红注射液对急性脑梗死患者sCD40L及超敏C-反应蛋白的影响%Efficacy of Danhong injection for patients with acute stage of cerebral infarction and its effects on serum sCD40L and hs-CRP levels

    Institute of Scientific and Technical Information of China (English)

    沈壮虹; 宋水江


    Objective To evaluate efficacy of Danhong injection for patients with acute stage of cerebral infarction and its effects on serum levels of soluble CD40 ligand (sCD40L) and high-sensitivity C-reactive protein(hs-CRP). Methods Ninety two patients with acute ischemic cerebral infarction were randomly assigned to receive Danhong injection (30ml/d, i.v drip, for 14d) in addition to routine treatment (Danhong group) or routine treatment only(control group).Serum sCD40L and hs-CRP were mea-sured, and Barthel index (BI) and Chinese stroke Scale (CSS) were assessed before and after treatment in both groups. Results The levels of sCD40L and hs-CRP were deceased after treatment in both groups, however, the levels in Danhong group were significantly lower than those in control group (P<0.05). The scores of CSS and BI of two groups were improved after treatment, while scores in Danhong group were better than those in control group (P<0.05). Conclusion Danhong injection can decrease serum levels of sCD40L and hs-CRP and improve the recovery of neural function for patients with acute cerebral infarction.%  目的探讨步长丹红注射液对急性脑梗死患者血清可溶性白细胞分化抗原40配体(sCD40L)及超敏 C-反应蛋白(hs-CRP)的影响及临床疗效。方法92例急性脑梗死患者分为两组,即常规治疗组和丹红治疗组,丹红治疗组在常规治疗基础上给予步长丹红注射液30ml 溶于0.9%氯化钠注射液250ml,1次/d,静脉滴注,共14d。治疗前后测定血 sCD40L 及 hs-CRP 的变化,并用中国卒中量表(CSS)及巴氏指数(BI)评定。结果两组患者 sCD40L 及 hs-CRP 均下降,丹红治疗组均明显低于常规治疗组(均 P<0.05)。治疗后两组 CSS 及 BI 评分较治疗前均明显增加,丹红治疗组均高于常规治疗组(均 P<0.05)。结论步长丹红注射液可降低急性脑梗死患者 sCD40L 及 hs-CRP 的水平,有益于患者神经功能的恢复。

  4. Combination of monoclonal antibodies with DST inhibits accelerated rejection mediated by memory T cells to induce long-lived heart allograft acceptance in mice. (United States)

    Shao, Wei; Chen, Jibing; Dai, Helong; Peng, Yuanzheng; Wang, Feng; Xia, Junjie; Thorlacius, Henrik; Zhu, Qi; Qi, Zhongquan


    Donor-reactive memory T cells mediated accelerated rejection is known as a barrier to the survival of transplanted organs. We investigated the combination of different monoclonal antibodies (mAbs) and donor-specific transfusion (DST) in memory T cells-based adoptive mice model. In the presence of donor-reactive memory T cells, the mean survival time (MST) of grafts in the anti-CD40L/LFA-1/DST group was 49.8d. Adding anti-CD44/CD70 mAbs to anti-CD40L/LFA-1/DST treatment. The MST was more than 100 d (MST>100 d). Compared with anti-CD40L/LFA-1/DST group, anti-CD40L/LFA-1/CD44/CD70/DST group notably reduced the expansion of memory T cells, enhanced the proportion of CD4+Foxp3+ regulatory T cells (Tregs) and suppressed donor-specific responses. Our data suggest that anti-CD40L/LFA-1/CD44/CD70mAbs and DST can synergistically inhibit accelerated rejection mediated by memory T cells to induce long-lived heart allograft acceptance in mice.

  5. 血清可溶性CD40L和C反应蛋白在慢性血透患者外周血管钙化的作用%Role of soluble CD40L and C-reactive protein in peripheral vascular calcification in patients undergoing of chronic hemodialysis

    Institute of Scientific and Technical Information of China (English)

    伍强; 孙艳; 杨铁城; 张海燕


    Objective To investigate the role of soluble CD40 ligand (sCD40L) and C-reactive protein (CRP) in peripheral vascular calcification in hemodialytic patients.Methods 40 hemodialytic patients with uremia underwent arteriovenous fistula reconstruction.The stumps of radial artery were removed for assessing vascular calcification.The patients were grouped according to the presence or absence of calcification and its degree.Serum levels of sCD40L and CRP were detected.The differences in levels of sCD40L and CRP were compared between calcification group and non-calcification group and between calcification groups at different degrees calcification.Results Radial artery calcification was detectable in 23 of the patients with calcium staining,9 of whom had severe calcification and the rest 14 had mild to moderate calcification.Levels of sCD40L and CRP were significantly higher in calcification group than in non-calcification group (P<0.01); they were also higher in severe calcification group than in mild to moderate calcification group (P<0.05).Levels of sCD40L were positively correlated with those of CRP.%目的 探讨血清可溶性白细胞分化抗原40配体(sCD40L)和C反应蛋白(CRP)在尿毒症血液透析患者外周血管钙化中的作用.方法 尿毒症血液透析患者40例因动静脉内瘘失功行内瘘重建术,术中取桡动脉残端行钙化染色观察血管钙化情况,依据血管钙化有无及程度分组,同时检测血清sCD40L和CRP水平,比较钙化组与非钙化组,不同程度钙化组间血清sCD40L和CRP水平的差异.结果 40例患者桡动脉钙化染色检出血管钙化23例,其中重度钙化9例,轻中度钙化14例,钙化组血清sCD40L和CRP水平高于非钙化组,有统计学差异(P<0.01).重度钙化组sCD40L和CRP水平高于轻中度钙化组.有统计学差异(P<0.05).血清sCD40L和CRP含量呈正相关.结论 sCD40L和炎症反应可能参与了尿毒症血液透析患者外周血管钙化的发生.

  6. B-NHL患者骨髓单个核细胞表面CD40、CD40L的表达及意义%Expressions and significance of CD40,CD40L in bone marrow mononuclear cell surface of patients with B-cell Non-Hodgkin′s Lymphoma

    Institute of Scientific and Technical Information of China (English)

    刘爱春; 任宏伟; 鄂明艳; 王燕


    目的:探讨B细胞非霍奇金淋巴瘤(B cell Non-Hodgkin′s Lymphoma,B-NHL)患者骨髓单个核细胞( BMMC)表面CD40、 CD40 L的表达情况及变化规律,分析CD40、CD40 L表达与淋巴瘤发病、侵袭性及预后的关系及意义。方法采集20例初诊B-NHL伴有骨髓侵犯的患者(实验组)的骨髓标本及12例健康者(对照组)的骨髓标本,分离单个核细胞,采用直接荧光抗体标记,应用流式细胞仪检测细胞表面CD40、CD40 L的表达情况。相关实验结果进行统计学比较。结果(1) B-NHL中CD40阳性率(45.78±3.82)%显著高于正常对照组(13.99±2.20)%,P<0.01;B-NHL中CD40L阳性率(3.44±0.88)%显著低于正常对照组(10.64±1.03)%,P<0.01;(2) B -NHL 伴有骨髓侵犯的患者CD40、CD40L阳性率与病理类型、LDH值、全身症状呈显著相关,P<0.05;(3) B-NHL伴有骨髓侵犯的患者中CD40与CD40L表达呈负相关,r =-0.47,P<0.05。结论(1) CD40、CD40L阳性率与病理类型、LDH值、全身症状密切相关,其可能与B-NHL的侵袭性及预后有关;(2) B-NHL患者中CD40表达的增高、CD40L表达的减少可能是影响其发病的因素之一;(3) B-NHL患者中CD40L表达的减少可能与肿瘤免疫逃逸机制有关。%Objective To explore the expressions and changing regularity of CD 40,CD40L in surface of bone marrow mononuclear cell (BMMC)of patients with B -cell Non-Hodgkin′s Lymphoma.To study the rela-tionship between the expressions of CD 40,CD40L and the pathogenesis、infestation、prognosis,clinical implication of patients with Lymphoma .Methods Twenty bone marrow specimens of B -NHL ( experimental group ) and twelve healthy bone marrow specimens(contiol group)were collected.To separate mononuclear cell,we used di-rect fluorescent antibody to mark cells ,the expressions of CD40 and CD40L were determined by flow cytometry

  7. Complexes between nuclear factor-κB p65 and signal transducer and activator of transcription 3 are key actors in inducing activation-induced cytidine deaminase expression and immunoglobulin A production in CD40L plus interleukin-10-treated human blood B cells. (United States)

    Lafarge, S; Hamzeh-Cognasse, H; Richard, Y; Pozzetto, B; Cogné, M; Cognasse, F; Garraud, O


    The signal transducer and activator of transcription 3 (STAT3) transcription factor pathway plays an important role in many biological phenomena. STAT3 transcription is triggered by cytokine-associated signals. Here, we use isolated human B cells to analyse the role of STAT3 in interleukin (IL)-10 induced terminal B cell differentiation and in immunoglobulin (Ig)A production as a characteristic readout of IL-10 signalling. We identified optimal conditions for inducing in-vitro IgA production by purified blood naive B cells using IL-10 and soluble CD40L. We show that soluble CD40L consistently induces the phosphorylation of nuclear factor (NF)-κB p65 but not of STAT3, while IL-10 induces the phosphorylation of STAT3 but not of NF-κB p65. Interestingly, while soluble CD40L and IL-10 were synergistic in driving the terminal maturation of B cells into IgA-producing plasma cells, they did not co-operate earlier in the pathway with regard to the transcription factors NF-κB p65 or STAT3. Blocking either NF-κB p65 or STAT3 profoundly altered the production of IgA and mRNA for activation-induced cytidine deaminase (AID), an enzyme strictly necessary for Ig heavy chain recombination. Finally, the STAT3 pathway was directly activated by IL-10, while IL-6, the main cytokine otherwise known for activating the STAT3 pathway, did not appear to be involved in IL-10-induced-STAT3 activation. Our results suggest that STAT3 and NF-κB pathways co-operate in IgA production, with soluble CD40L rapidly activating the NF-κB pathway, probably rendering STAT3 probably more reactive to IL-10 signalling. This novel role for STAT3 in B cell development reveals a potential therapeutic or vaccine target for eliciting IgA humoral responses at mucosal interfaces.

  8. 血清Hcy、sCD40L及LDL-C与冠状动脉支架内再狭窄的相关性研究%Postprocedural serum Hcy, sCD40L and LDL-C are associated with coronary in-stent restenosis in patients with drug-coated stent implantation

    Institute of Scientific and Technical Information of China (English)

    陈玉映; 胡允兆; 陈盈文; 何宗云; 郑素琳; 吴焱贤


    目的:探讨血清同型半胱氨酸(Hcy)、LDL-C、可溶性白细胞表面抗原40配体(sCD40L)等因素在冠状动脉支架内再狭窄发生过程中的临床意义.方法:收集冠状动脉药物涂层支架植入术后因胸痛再发/术后6个月常规行冠状动脉造影随访患者共120例,其中88例造影未出现支架内再狭窄(对照组),32例出现再狭窄(再狭窄组),回顾分析两组患者的年龄、性别、高血压病史、糖尿病史、心肌梗死病史及冠心痛家族史,收集患者支架植入术后1周以及胸痛再发/术后6个月冠状动脉造影检查这两个时间点的BMI、肾小球滤过率(GFP)、甘油三酯、总胆固醇、糖化血红蛋白( GHbA1c)、LDL-C、HDL-C、Hcy、sCD40L等指标.结果:两组患者在支架植入术后1周各指标比较差异无统计学意义,因胸痛再发/术后6个月行冠状动脉造影随访时发现再狭窄组的LDL-C、Hey、sCD40L和对照组比较差异有统计学意义(P<0.01),二分类变量Logistic回归分析显示,LDL-C、sCD40L及Hcy的升高会增加再狭窄的风险,且Hcy与LDL-C(r=0.36,P=0.002)、sCD40L(r=0.27,P=0.001)呈正相关.结论:支架植入术后LDL-C、Hcy、sCD40L升高是支架内再狭窄的危险因子,并且Hcy与LDL-C、sCD40L呈正相关.%Objective: To evaluate the roles of serum homocysteine ( Hey), low density lipoprotein cholesterol (LDL-C) and soluble leukocyte surface antigens 40 ligand (sCD40L) in in-stent restenosis (ISR) after successful primary percutaneous coronary intervention (PCI). Methods; Body mass index (BMI) , glomerular filtration rate (GFP) , total triglycerides (TG) , total cholesterol (TC) , glycosylated hemoglobin (GHbAlc) , LDL-C, high density lipoprotein ( HDL-C) , Hey and sCD40L levels were measured in 120 consecutive patients 1 week and 6 months ( or chest pain occurred) after PCI. These patients were grouped as ISR and non-ISR based on angiography during follow-up time. Besides, age, sex, hypertension, diabetes

  9. 孕妇血中可溶性细胞分化抗原40L、肿瘤坏死因子α水平变化与早发型子痫前期的关系%Relation of plasma level of sCD40L and serum level TNF-α with early onset preeclampsia

    Institute of Scientific and Technical Information of China (English)

    尹洁; 史丽; 赵喜娃; 李青梅; 董晓静; 王娟; 姜秉芬


    Objective To study changes of plasma level of sCD40L and serum level of tumor necrosis factor-a(TNF-α) in patients with early onset preeclampsia,To investigate the relationship of sCD40L、TNF-α and clinical data in early onset preeclampsia.Methods The enzyme-linked immunosorbent assay between June 2011 and September 2012 at The Fourth Clinical Medical College of Hebei Medical University in patients with early-onset preeclampsia 64cases,(mild preeclampsia 30 cases and severe preeclampsia patients 34 cases),and randomly selected 20 cases of normal late pregnancy in plasma levels of sCD40L and serum level of TNF-α.At the same time,blood biochemical in dexes (BBI) were measured.Results The level of sCD40L and TNF-α in women with mild and severe early onset preeclampsia were significantly higher than that in normal controls; The level of sCD40L and TNF-α in women with severe early onset preeclampsia were significantly higher than that in mild early onset preeclampsia,P < 0.01.The plasma levels of sCD40L were obviously positively correlated with the serum level of TNF-α in patients with early onset preeclampsia,r =0.967,P < 0.001.The level of sCD40L、TNF-α in early onset preeclampsia were obviously positively correlated with the levels of 24-hurineprotein,SBP,DBP,MAP,BUN,and negatively correlated with serum albumin; whereas that had no significant correlation with UA,34 cases severe preeclampsia happen eclampsia postpartum,the average plasma sCD40L level of 4 cases were 9.65μg/L.Conclusion Expression of sCD40L,TNF-α in early-onset preeclampsia is high and associates with the severity of the disease,they could be used in detecting and monitoring for early onset preeclampsia.%目的 探讨孕妇血中可溶性细胞分化抗原40L(sCD40L)、肿瘤坏死因子α(TNF-α)水平变化与早发型子痫前期的发病及临床指标的相关性.方法 选择2011年6月至2012年9月在河北医科大学第四医院分娩的早发型子痫前期患者64

  10. DNA Profiling of Convicted Offender Samples for the Combined DNA Index System (United States)

    Millard, Julie T


    The cornerstone of forensic chemistry is that a perpetrator inevitably leaves trace evidence at a crime scene. One important type of evidence is DNA, which has been instrumental in both the implication and exoneration of thousands of suspects in a wide range of crimes. The Combined DNA Index System (CODIS), a network of DNA databases, provides…

  11. Effcet of atorvastatin on the expression of MMP-8, CD40L and proliferation of intima in artery injured%阿托伐他汀对鼠颈总动脉血管损伤后CD40L和MMP-8表达影响

    Institute of Scientific and Technical Information of China (English)

    刘群威; 周胜华; 海志杰


    Objective To observe the expression of MMP-8 and CD40L in serum in rats and the effect of statin on their expression and vascular intima proliferation after angioplasty. Methods The models of rat were prepared and divided into three groups which were the operation group drug-intervention group and the control. The level of MMP-8 and CD40L in serum and proliferation of intima were detected in the three groups after angioplasty and intervention of atorvastatin. The methods of measurement included ELISA for the serum level of MMP-8 and CD40L Results Compared with the control group, the operation group showed increased in the expression of MMP-8 and CD40L (0. 97 ±0. 11 ng/ml vs. 2. 13 ±0. 27 ng/ml,9. 12 ± 1. 39 ng/ml vs. 23. 47 ±3. 95 ng/ml,P <0. 01 respectively), with the apparent proliferation of intima one week later [ (18. 90 ± 1. 36) x 103 μm2 vs. (69. 13 ±4. 38) x 103 μm2 ,P <0.01 ] , which were found to be reduced in the atorvastatin group after treatment [ (142. 65 + 5. 45) x 103 μm2 vs. ( 81. 76 ± 4. 35 ) x 103 uV,P<0.05]. The expression of MMP-8 and CD40L were inhibited [(2. 13 ±0.27) ng/ml vs. (1. 37 ± 0.19) ng/ml, (23.47 ±3.95) ng/ml us. (14.48 ±2.08) ng/ml, P < 0.05 ], respectively); and proliferation of intima were enhanced more in the operation group after two weeks [ (142. 65 ± 5. 45 ) x 103 μm2 vs. (81. 76 ±4. 35) x 103 μm2 , P <0. 01 ]. Conclusions The expression of MMP-8 and CD40L in rat models were increaced after angioplasty, which may be related to vascular intima proliferation and reconstruction. Atorvastatin can suppress expression of MMP-8 and CD40L and reduces vascular intima proliferation after angioplasty.%目的 观察在鼠颈总动脉血管损伤后血中CD40L、MMP-8水平和血管内膜增生情况以及他汀类药物干预后的影响.方法 在鼠颈总动脉血管损伤模型上观察血管损伤及阿托伐他汀干预后的内膜增生情况,并应用ELISA方法检测血管损伤及阿托伐他汀干预后CD40L

  12. Changes of levels of plasma sCD40L,MMP-9 and TIMP-1 in patients with acute coronary syndrome and their clinical significance%急性冠脉综合征患者血浆sCD40L与血清基质金属蛋白酶水平的变化及其意义

    Institute of Scientific and Technical Information of China (English)

    赵晓辉; 王皓娟; 李淑红; 牟春平


    Objective: To investigate changes of levels of soluble CD40 ligand (sCD40L), serum matrix metalloprotein-ase—9 (MMP—9) and serum tissue inhibitor of metalloproteinases — 1 (TIMP— 1) in patients with acute coronary syndrome (ACS) and their correlation. Methods: Enzyme—linked immunosorbent assay was used to measure levels of sCD40L, MMP—9 and TIMP—1 in 70 patients with coronary heart disease (CHD) [35 ACS cases, 35 cases with stable angina pectoris (SAP)] and 35 non— CHD patients (normal control group). Results: Compared with normal control group and SAP group, the levels of sCD40L [ (2. 73±0. 92) μg/ml vs. (3. 05±0. 98) μg/ml vs. (4. 72±1. 15) pig/ml] and MMP-9 [ (152. 38±54. 22) ng/ml vs. (341. 12±69. 96) ng/ml vs. (574. 2±139. 20) ng/ml] significantly increased, and level of TIMP-1 [ (415. 92±13. 96) ng/ml vs. (249. 32±36. 80) ng/ml vs. (172. 20±40. 10) ng/ml] significantly decreased in ACS group, P<0. 01 all; MMP—9 level was positively correlated with sCD40L level (r=0. 42, P<0. 05). Conclusion: Increased levels of sCD40L and serum MMP—9 and decreased serum TIMP—1 level in ACS patients may be related with instability of atheromatous plaque, and they could serve as serological indicators for instability of atheromatous plaque.%目的:观察急性冠脉综合征(ACS)患者可溶性CD40配体(sCD40L)及血清基质金属蛋白酶-9(MMP-9)、血清组织金属蛋白酶抑制物-1(TIMP-1)水平变化及其相关性.方法:采用酶联免疫吸附法测定70例冠心病患者[ACS患者35例、稳定型心绞痛(SAP)患者35例]、35例非冠心病患者(正常对照组)sCD40L、MMP-9,TIMP-1的水平.结果:与正常对照组及SAP组比较,ACS组sCD40L[(2.73±0.92)μg/ml比(3.05±0.98)μg/ml比(4.72±1.15)μg/ml]、MMP-9[(152.38±54.22)ng/ml比(341.12±69.96)ng/ml比(574.2±139.20)ng/ml]水平明显升高(P均<0.01),而TIMP-1[(415.92±13.96)ng/ml比(249.32±36.80)ng/ml比(172.20±40.10)ng/ml]水平明显降低(P<0.01);且MMP-9

  13. RNA干扰技术阻断CD40/CD40L共刺激通路对小鼠移植心存活时间的影响%Effects of blocking CD40/CD40L costimulatory pathway by RNA interference on the survival of mouse cardiac allograft

    Institute of Scientific and Technical Information of China (English)

    朱杰昌; 付蔚华; 朱理玮


    Objective To investigate the effect of blocking CD40/CD40L costimulatory pathway by the lentiviral vector-mediated RNA interference on the survival of mouse cardiac allograft. Methods Mouse bone marrow-derived dendritic cells (DCs) were infected by CD40-RNAi lentiviral vector in vitro, and tolerogenic DCs (Tol-DCs) with decreased CD40 expression were prepared. Fluorescence real-time quantitative PCR and flow cytometry were used to analyze the expression of CD40 mRNA and DC surface antigens CD40, CD11c, MHC Ⅱ before and after infection. Mouse model of heterotropic abdominal heart transplantation was established. Seven days prior to heart transplantation, Tol-DCs with decreased CD40 expression were transfused into recipient mice intravenously (lentivirus infected DC group). Control group and non-infected DC group were assigned simultaneously. The survival of cardiac allograft was monitored and pathological grade of acute rejection 7 days after heterotropic abdominal heart transplantation was determined. Results The transcription of CD40 mRNA of DCs was down-regulated significantly at 48 h after CD40-RNAi lentiviral vector infection, and the inhibition rate was 80. 9%. The expression of CD40 protein was also significantly decreased as compared with control group (40. 07% ± 4. 03% ) ( P < 0. 05 ).Compared to control group (8 ± 2 days) and non-infected DC group (9 ± 1 days), the survival time of cardiac allograft in CD40-RNAi lentivirus infected DC group (14 ± 4 days) was significantly prolonged (P< 0. 05 ), and the pathological grade of acute rejection decreased significantly ( P < 0. 05 ).Conclusion Blocking CD40/CD40L costimulatory pathway could hamper the activation of allogeneic T lymphocyte, inhibit the acute rejection and prolong the survival of mouse cardiac allograft.%目的 探讨慢病毒介导RNA干扰(RNAi)技术阻断CD40/CD40L共刺激通路对小鼠移植心存活时间的影响.方法 以针对小鼠CD40基因的RNAi慢病毒载体在体外

  14. Combinative exposure effect of radio frequency signals from CDMA mobile phones and aphidicolin on DNA integrity. (United States)

    Tiwari, R; Lakshmi, N K; Surender, V; Rajesh, A D V; Bhargava, S C; Ahuja, Y R


    The aim of present study is to assess DNA integrity on the effect of exposure to a radio frequency (RF) signal from Code Division Multiple Access (CDMA) mobile phones. Whole blood samples from six healthy male individuals were exposed for RF signals from a CDMA mobile phone for 1 h. Alkaline comet assay was performed to assess the DNA damage. The combinative exposure effect of the RF signals and APC at two concentrations on DNA integrity was studied. DNA repair efficiency of the samples was also studied after 2 h of exposure. The RF signals and APC (0.2 microg/ml) alone or in synergism did not have any significant DNA damage as compared to sham exposed. However, univariate analysis showed that DNA damage was significantly different among combinative exposure of RF signals and APC at 0.2 microg/ml (p < 0.05) and at 2 microg/ml (p < 0.02). APC at 2 microg/ml concentration also showed significant damage levels (p < 0.05) when compared to sham exposed. DNA repair efficiency also varied in a significant way in combinative exposure sets (p < 0.05). From these results, it appears that the repair inhibitor APC enhances DNA breaks at 2 microg/ml concentration and that the damage is possibly repairable. Thus, it can be inferred that the in vitro exposure to RF signals induces reversible DNA damage in synergism with APC.

  15. A combined HM-PCR/SNuPE method for high sensitive detection of rare DNA methylation

    Directory of Open Access Journals (Sweden)

    Tierling Sascha


    Full Text Available Abstract Background DNA methylation changes are widely used as early molecular markers in cancer detection. Sensitive detection and classification of rare methylation changes in DNA extracted from circulating body fluids or complex tissue samples is crucial for the understanding of tumor etiology, clinical diagnosis and treatment. In this paper, we describe a combined method to monitor the presence of methylated tumor DNA in an excess of unmethylated background DNA of non-tumorous cells. The method combines heavy methyl-PCR, which favors preferential amplification of methylated marker sequence from bisulfite-treated DNA with a methylation-specific single nucleotide primer extension monitored by ion-pair, reversed-phase, high-performance liquid chromatography separation. Results This combined method allows detection of 14 pg (that is, four to five genomic copies of methylated chromosomal DNA in a 2000-fold excess (that is, 50 ng of unmethylated chromosomal background, with an analytical sensitivity of > 90%. We outline a detailed protocol for the combined assay on two examples of known cancer markers (SEPT9 and TMEFF2 and discuss general aspects of assay design and data interpretation. Finally, we provide an application example for rapid testing on tumor methylation in plasma DNA derived from a small cohort of patients with colorectal cancer. Conclusion The method allows unambiguous detection of rare DNA methylation, for example in body fluid or DNA isolates from cells or tissues, with very high sensitivity and accuracy. The application combines standard technologies and can easily be adapted to any target region of interest. It does not require costly reagents and can be used for routine screening of many samples.

  16. DNA quantification based on FRET realized by combination with surfactant CPB. (United States)

    Liu, Chunxia; Wang, Lei; Jiang, Wei


    In this work, we developed a novel DNA quantitative analysis based on fluorescence resonance energy transfer (FRET) realized by combination with a surfactant CPB. The approach was capable of detecting long-stranded DNA in a separation-free format. A sandwich-type FAM-c-DNA-t-DNA-r-DNA-TAMRA conjugate was first formed by the capture probe tagged with FAM, the reporter probe tagged with TAMRA and the target DNA through hybridization. The donor (FAM) and the acceptor (TAMRA) were bridged to afford a FRET system. Subsequently, an addition of the cationic surfactant CPB to the system resulted in a substantial change of the microenvironment and an effective condensation of DNA strands. Consequently, without altering the component of the double strands, an enhanced acceptor fluorescence signal from FRET was achieved and a quantification of the target DNA containing 30 bases was enabled. Under the optimal experimental conditions, an excellent linear relationship between the increase of acceptor fluorescent peak area and the target DNA concentration was obtained over the range from 1.0 x 10(-7) to 3.0 x 10(-9) mol L(-1). The proposed approach offered adequate sensitivity for the detection of the target DNA at 1.0 x 10(-9) mol L(-1).

  17. Efficient vaccine against pandemic influenza: combining DNA vaccination and targeted delivery to MHC class II molecules. (United States)

    Grødeland, Gunnveig; Bogen, Bjarne


    There are two major limitations to vaccine preparedness in the event of devastating influenza pandemics: the time needed to generate a vaccine and rapid generation of sufficient amounts. DNA vaccination could represent a solution to these problems, but efficacy needs to be enhanced. In a separate line of research, it has been established that targeting of vaccine molecules to antigen-presenting cells enhances immune responses. We have combined the two principles by constructing DNA vaccines that encode bivalent fusion proteins; these target hemagglutinin to MHC class II molecules on antigen-presenting cells. Such DNA vaccines rapidly induce hemagglutinin-specific antibodies and T cell responses in immunized mice. Responses are long-lasting and protect mice against challenge with influenza virus. In a pandemic situation, targeted DNA vaccines could be produced and tested within a month. The novel DNA vaccines could represent a solution to pandemic preparedness in the advent of novel influenza pandemics.

  18. DNA damage in peripheral blood lymphocytes in patients during combined chemotherapy for breast cancer

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez-Suarez, Patricia [Oncological Research Unit, Oncology Hospital, National Medical Center S-XXI, Instituto Mexicano del Seguro Social (IMSS), Av. Cuauhtemoc 330, Col. Doctores, 06725 Mexico, D.F. (Mexico); Ostrosky-Wegman, Patricia [Biomedical Research Institute, Universidad Nacional Autonoma de Mexico (UNAM), Mexico City (Mexico); Gallegos-Hernandez, Francisco [Department of Clinical Oncology, Oncology Hospital, National Medical Center S-XXI, Instituto Mexicano del Seguro Social (IMSS), Mexico City (Mexico); Penarroja-Flores, Rubicelia; Toledo-Garcia, Jorge [Oncological Research Unit, Oncology Hospital, National Medical Center S-XXI, Instituto Mexicano del Seguro Social (IMSS), Av. Cuauhtemoc 330, Col. Doctores, 06725 Mexico, D.F. (Mexico); Bravo, Jose Luis [Atmospheric Sciences Institute, Universidad Nacional Autonoma de Mexico (UNAM), Mexico City (Mexico); Rojas del Castillo, Emilio [Biomedical Research Institute, Universidad Nacional Autonoma de Mexico (UNAM), Mexico City (Mexico); Benitez-Bribiesca, Luis [Oncological Research Unit, Oncology Hospital, National Medical Center S-XXI, Instituto Mexicano del Seguro Social (IMSS), Av. Cuauhtemoc 330, Col. Doctores, 06725 Mexico, D.F. (Mexico)], E-mail:


    Combined chemotherapy is used for the treatment of a number of malignancies such as breast cancer. The target of these antineoplastic agents is nuclear DNA, although it is not restricted to malignant cells. The aim of the present study was to assess DNA damage in peripheral blood lymphocytes (PBLs) of breast cancer patients subjected to combined adjuvant chemotherapy (5-fluorouracil, epirubicin and cyclophosphamide, FEC), using a modified comet assay to detect DNA single-strand breaks (SSB) and double-strand breaks (DSB). Forty-one female patients with advanced breast cancer before and after chemotherapy and 60 healthy females participated in the study. Alkaline and neutral comet assays were performed in PBLs according to a standard protocol, and DNA tail moment was measured by a computer-based image analysis system. Breast cancer patients before treatment had higher increased background levels of SSB and DSB as compared to healthy women. During treatment, a significant increase in DNA damage was observed after the 2nd cycle, which persisted until the end of treatment. Eighty days after the end of treatment the percentage of PBLs with SSB and DSB remained elevated, but the magnitude of DNA damage (tail moment) returned to baseline levels. There was no correlation between PBL DNA damage and response to chemotherapy. DNA-SSB and DSB in PBLs are present in cancer patients before treatment and increase significantly after combined chemotherapy. No correlation with response to adjuvant chemotherapy was found. Biomonitoring DNA damage in PBLs of cancer patients could help prevent secondary effects and the potential risks of developing secondary cancers.


    Institute of Scientific and Technical Information of China (English)


    In the present study, eight combinations of restriction enzymes and oligonucleotide probes were tested for detecting VNTR polymorphism. More than a hundred loci were detected by all enzyme-probe combi nations. The influences of breed, enzyme and probe as well as their interactions were analysed, and the mean value of DNA fingerprint data was calculated for the enzymes and probes. The results will provide some valu- able information for studying the genetic relationship of individuals or populations using DNA fingerprinting.

  20. Low-density lipoprotein peptide-combined DNA nanocomplex as an efficient anticancer drug delivery vehicle. (United States)

    Zhang, Nan; Tao, Jun; Hua, Haiying; Sun, Pengchao; Zhao, Yongxing


    DNA is a type of potential biomaterials for drug delivery due to its nanoscale geometry, loading capacity of therapeutics, biocompatibility, and biodegradability. Unfortunately, DNA is easily degraded by DNases in the body circulation and has low intracellular uptake. In the present study, we selected three cationic polymers polyethylenimine (PEI), hexadecyl trimethyl ammonium bromide (CTAB), and low-density lipoprotein (LDL) receptor targeted peptide (RLT), to modify DNA and improve the issues. A potent anti-tumor anthracycline-doxorubicin (DOX) was intercalated into DNA non-covalently and the DOX/DNA was then combined with PEI, CTAB, and RLT, respectively. Compact nanocomplexes were formed by electrostatic interaction and could potentially protect DNA from DNases. More importantly, RLT had the potential to enhance intracellular uptake by LDL receptor mediated endocytosis. In a series of in vitro experiments, RLT complexed DNA enhanced intracellular delivery of DOX, increased tumor cell death and intracellular ROS production, and reduced intracellular elimination of DOX. All results suggested that the easily prepared and targeted RLT/DNA nanocomplexes had great potential to be developed into a formulation for doxorubicin with enhanced anti-tumor activity.

  1. [Combined hopping-superexchange mechanism of charge transfer in DNA; a model with nearest interactions]. (United States)

    Lakhno, V D; Sultanov, V B


    In the framework of the earlier developed combined hopping-superexchange mechanism of charge transfer in DNA, a model with all nearest interactions between nucleobases is proposed. It is shown that the transfer rates for various types of nucleotide sequences calculated within this model are in a good agreement with experimental data.

  2. Combining bleach and mild predigestion improves ancient DNA recovery from bones

    DEFF Research Database (Denmark)

    Boessenkool, Sanne; Hanghøj, Kristian Ebbesen; Nistelberger, Heidi M.


    aimed to improve ancient DNA recovery before library amplification have recently been developed. Here, we test the effects of combining two of such protocols, a bleach wash and a predigestion step, on 12 bone samples of Atlantic cod and domestic horse aged 750-1350 cal. years before present. Using high...

  3. Enhancement of the priming efficacy of DNA vaccines encoding dendritic cell-targeted antigens by synergistic toll-like receptor ligands

    Directory of Open Access Journals (Sweden)

    Kornbluth Richard S


    Full Text Available Abstract Background Targeting of protein antigens to dendritic cells (DC via the DEC205 receptor enhances presentation of antigen-derived peptides on MHC-I and MHC-II molecules and, in the presence of costimulatory signals, antigen-specific immune responses. The immunogenicity and efficacy of DNA vaccination can also be enhanced by fusing the encoded antigen to single chain antibodies directed against DEC205. To further improve this strategy, we evaluated different toll-like receptor ligands (TLR and CD40 ligands (CD40L as adjuvants for DNA vaccines encoding a DEC205-single-chain antibody fused to the ovalbumin model antigen or HIV-1 Gag and assessed the priming efficacy of DNA in a DNA prime adenoviral vector boost immunization regimen. Results Mice were primed with the adjuvanted DEC-205 targeted DNA vaccines and boosted with adenoviral vectors encoding the same antigens. CD8+ T cell responses were determined after the adenoviral booster immunization, to determine how well the different DNA immunization regimens prime for the adenoviral boost. In the absence of adjuvants, targeting of DNA-encoded ovalbumin to DCs suppressed CD8+ T-cell responses after the adenoviral booster immunization. CD8+ T-cell responses to the DEC205 targeted DNA vaccines increased only slightly by adding either the TLR-9 ligand CpG, the TLR-3 ligand Poly I:C, or CD40 ligand expression plasmids. However, the combination of both TLR-ligands led to a strong enhancement of CD8+ T-cell responses compared to a non-targeted DNA vaccine. This finding was confirmed using HIV Gag as antigen. Conclusion Although DNA prime adenoviral vector boost immunizations belong to the strongest inducers of cytotoxic T cell responses in different animal models and humans, the CD8+ T cell responses can be further improved by targeting the DNA encoded antigen to DEC205 in the presence of synergistic TLR ligands CpG and Poly I:C.

  4. Synergistic DNA-damaging effect in multiple myeloma with the combination of zalypsis, bortezomib and dexamethasone (United States)

    López-Iglesias, Ana-Alicia; González-Méndez, Lorena; San-Segundo, Laura; Herrero, Ana B.; Hernández-García, Susana; Martín-Sánchez, Montserrat; Gutiérrez, Norma C.; Paíno, Teresa; Avilés, Pablo; Mateos, María-Victoria; San-Miguel, Jesús F.; Garayoa, Mercedes; Ocio, Enrique M.


    Despite new advances in multiple myeloma treatment and the consequent improvement in overall survival, most patients relapse or become refractory to treatment. This suggests that new molecules and combinations that may further inhibit important survival pathways for these tumor cells are needed. In this context, zalypsis is a novel compound, derived from marine organisms, with a powerful preclinical anti-myeloma effect based on the sensitivity of malignant plasma cells to DNA-damage induction; and it has already been tested in a phase I/II clinical trial in multiple myeloma. We hypothesized that the addition of this compound to the combination of bortezomib plus dexamethasone may improve efficacy with acceptable toxicity. The triple combination demonstrated strong synergy and higher efficacy compared with double combinations; not only in vitro, but also ex vivo and, especially, in in vivo experiments. The triple combination triggers cell death, mainly through a synergistic induction of DNA damage and a decrease in the nuclear localization of nuclear factor kappa B. Our findings support the clinical evaluation of this combination for relapsed and refractory myeloma patients. PMID:27540138

  5. Nanoparticles and DNA - a powerful and growing functional combination in bionanotechnology (United States)

    Samanta, Anirban; Medintz, Igor L.


    Functionally integrating DNA and other nucleic acids with nanoparticles in all their different physicochemical forms has produced a rich variety of composite nanomaterials which, in many cases, display unique or augmented properties due to the synergistic activity of both components. These capabilities, in turn, are attracting greater attention from various research communities in search of new nanoscale tools for diverse applications that include (bio)sensing, labeling, targeted imaging, cellular delivery, diagnostics, therapeutics, theranostics, bioelectronics, and biocomputing to name just a few amongst many others. Here, we review this vibrant and growing research area from the perspective of the materials themselves and their unique capabilities. Inorganic nanocrystals such as quantum dots or those made from gold or other (noble) metals along with metal oxides and carbon allotropes are desired as participants in these hybrid materials since they can provide distinctive optical, physical, magnetic, and electrochemical properties. Beyond this, synthetic polymer-based and proteinaceous or viral nanoparticulate materials are also useful in the same role since they can provide a predefined and biocompatible cargo-carrying and targeting capability. The DNA component typically provides sequence-based addressability for probes along with, more recently, unique architectural properties that directly originate from the burgeoning structural DNA field. Additionally, DNA aptamers can also provide specific recognition capabilities against many diverse non-nucleic acid targets across a range of size scales from ions to full protein and cells. In addition to appending DNA to inorganic or polymeric nanoparticles, purely DNA-based nanoparticles have recently surfaced as an excellent assembly platform and have started finding application in areas like sensing, imaging and immunotherapy. We focus on selected and representative nanoparticle-DNA materials and highlight their

  6. DNA binding protein identification by combining pseudo amino acid composition and profile-based protein representation (United States)

    Liu, Bin; Wang, Shanyi; Wang, Xiaolong


    DNA-binding proteins play an important role in most cellular processes. Therefore, it is necessary to develop an efficient predictor for identifying DNA-binding proteins only based on the sequence information of proteins. The bottleneck for constructing a useful predictor is to find suitable features capturing the characteristics of DNA binding proteins. We applied PseAAC to DNA binding protein identification, and PseAAC was further improved by incorporating the evolutionary information by using profile-based protein representation. Finally, Combined with Support Vector Machines (SVMs), a predictor called iDNAPro-PseAAC was proposed. Experimental results on an updated benchmark dataset showed that iDNAPro-PseAAC outperformed some state-of-the-art approaches, and it can achieve stable performance on an independent dataset. By using an ensemble learning approach to incorporate more negative samples (non-DNA binding proteins) in the training process, the performance of iDNAPro-PseAAC was further improved. The web server of iDNAPro-PseAAC is available at


    Institute of Scientific and Technical Information of China (English)

    MA Ping; YIN Yuan-qin; WANG Xiao-hua


    Objective: To investigate the expressions of cyclin D1 and p27 and DNA content in esophageal cancer and adjacent normal tissues, and to discuss the relationship between them. Methods: The cyclinD1 and p27 were detected by immunohistochemical staining; DNA content was measured by flow cytometry. Results: The positive expression rates of cyclinD1 and p27 in cancer were 45.8% and 33.3% respectively, the DNA content in the positive group of cyclinD1 was higher than that in the negative group of cyclinD1(1.54(0.21 versus 1.08(0.43, P<0.05), while the DNA content and SPF (S-phase fraction) in the positive group of p27 were lower than those in the negative group (1.10(0.19 and 5.56%(5.18% versus 1.66(0.28 and 19.78%(6.12%, P<0.05). Conclusion: The data show that the expression of cyclinD1 and p27 are related to the ontogenesis and progression of esophageal cancer. The combined detection of cyclinD1, p27 and DNA content may be indicators of diagnosis and assessment of esophageal cancer.

  8. Combined-dynamic mode"dip-pen" nanolithography and physically nanopatterning along single DNA molecules

    Institute of Scientific and Technical Information of China (English)

    LI Bin; WANG Ying; WU Haiping; ZHANG Yi; ZHANG Zhixiang; ZHOU Xingfei; LI Minqian; HU Jun


    Atomic force micriscope (AFM)-based dip-pen nanolithography (DPN) is an emerging approach for constructing nanostructures on material surfaces such as gold, silicon and silicon oxide. Although DPN is a powerful technique, it has not shown its ability of direct-writing and patterning of nanostructures on surfaces of soft materials, for example biomacromolecules. Direct depositing on soft surfaces becomes possible with the introduction of a combined-dynamic mode DPN rather than mostly used contact mode DPN or tapping mode DPN. In this report, the combined dynamic mode DPN is used for direct depositing protein ink on DNA molecules at the nanometer scale.

  9. Idelalisib and bendamustine combination is synergistic and increases DNA damage response in chronic lymphocytic leukemia cells. (United States)

    Modi, Prexy; Balakrishnan, Kumudha; Yang, Qingshan; Wierda, William G; Keating, Michael J; Gandhi, Varsha


    Idelalisib is a targeted agent that potently inhibits PI3Kδ which is exclusively expressed in hematological cells. Bendamustine is a well-tolerated cytotoxic alkylating agent which has been extensively used for treatment of chronic lymphocytic leukemia (CLL). Both these agents are FDA-approved for CLL. To increase the potency of idelalisib and bendamustine, we tested their combination in primary CLL lymphocytes. While each compound alone produced a moderate response, combination at several concentrations resulted in synergistic cytotoxicity. Idelalisib enhanced the bendamustine-mediated DNA damage/repair response, indicated by the phosphorylation of ATM, Chk2, and p53. Each drug alone activated γH2AX but combination treatment further increased the expression of this DNA damage marker. Compared with the control, idelalisib treatment decreased global RNA synthesis, resulting in a decline of early-response and short-lived MCL1 transcripts. In concert, there was a decline in total Mcl-1 protein in CLL lymphocytes. Isogenic mouse embryonic fibroblasts lacking MCL1 had higher sensitivity to bendamustine alone or in combination compared to MCL1 proficient cells. Collectively, these data indicate that bendamustine and idelalisib combination therapy should be investigated for treating patients with CLL.

  10. Augmentation of French grunt diet description using combined visual and DNA-based analyses (United States)

    Hargrove, John S.; Parkyn, Daryl C.; Murie, Debra J.; Demopoulos, Amanda W.J.; Austin, James D.


    Trophic linkages within a coral-reef ecosystem may be difficult to discern in fish species that reside on, but do not forage on, coral reefs. Furthermore, dietary analysis of fish can be difficult in situations where prey is thoroughly macerated, resulting in many visually unrecognisable food items. The present study examined whether the inclusion of a DNA-based method could improve the identification of prey consumed by French grunt, Haemulon flavolineatum, a reef fish that possesses pharyngeal teeth and forages on soft-bodied prey items. Visual analysis indicated that crustaceans were most abundant numerically (38.9%), followed by sipunculans (31.0%) and polychaete worms (5.2%), with a substantial number of unidentified prey (12.7%). For the subset of prey with both visual and molecular data, there was a marked reduction in the number of unidentified sipunculans (visual – 31.1%, combined &ndash 4.4%), unidentified crustaceans (visual &ndash 15.6%, combined &ndash 6.7%), and unidentified taxa (visual &ndash 11.1%, combined &ndash 0.0%). Utilising results from both methodologies resulted in an increased number of prey placed at the family level (visual &ndash 6, combined &ndash 33) and species level (visual &ndash 0, combined &ndash 4). Although more costly than visual analysis alone, our study demonstrated the feasibility of DNA-based identification of visually unidentifiable prey in the stomach contents of fish.

  11. Designing and constructing an 100 bp DNA Ladder by combining PCR and enzyme digestion methods

    Directory of Open Access Journals (Sweden)

    Saidijam M


    Full Text Available "n Normal 0 false false false EN-US X-NONE AR-SA MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:Arial; mso-bidi-theme-font:minor-bidi;} Background: Molecular DNA markers are one of the most important tools in molecular biology labs. The size of DNA molecules is determined by comparing them with known bands of markers during gel electrophoresis. There are many different protocols to produce these kinds of molecular markers. In this study we have suggested an efficient strategy to produce molecular weight markers in industrial proportions."n"nMethods : To achieve the desired sizes of DNA fragments, a combination of two previously known methods, restriction enzyme digestion and polymerase chain reaction (PCR, were used. The enzymatic digestion process was based on designing and constructing plasmids which equaled in size with the desired length of DNA fragments and produced the desired DNA fragment upon linearization. In the PCR method, the desired length of DNA fragments were cloned in multiple cloning sites of pTZ57R plasmid and in a PCR reaction, the new constructed plasmid was used as a template to produce the final fragment."n"nResults : Upon application of this strategy, 2000 and 3000 bp DNA fragments were produced by enzymatic digestion of plasmids of the same size. Moreover, 100 to 1500 bp fragments were produced during PCR using only a set of

  12. Combination chemotherapy of cancer using the inhibitor of DNA methylation 5-aza-2'-deoxycytidine (decitabine

    Directory of Open Access Journals (Sweden)

    Stephan L


    Full Text Available The epigenetic alterations marked by DNA methylation contribute to the malignant transformation of cells by silencing critical genes responsible for the regulation of growth. The potent DNA methylation inhibitor 5-aza-2’-deoxycytidine (decitabine; DAC has shown effectiveness in patients with myeloid malignancies. However, the responses are of short duration. The effectiveness of the DAC therapy may be limited by its incapacity to reactivate enough tumor suppressor genes. Other epigenetic mechanisms, such as the histone modification of target genes, may also hinder gene reactivation by DAC. The dose limiting toxicity of DAC is myelosuppression, which limits the duration of this therapy for clinical use. The clinical effectiveness of DAC may be enhanced by its use in combination with other agents that have diverse mechanisms of action. In this literature review, we summarize the results of preclinical and recent clinical trials of DAC used in combination with other agents to treat cancer. This review was conducted by searching online databases to analyze the available evidence regarding this area of interest. We looked at the combination of DAC with other epigenetic agents, cytotoxic agents, tyrosine kinase inhibitors, biochemical modulators and non-toxic agents. The data compiled suggests that combination epigenetic therapy is feasible, moderately toxic and has promising clinical potential. Preclinical studies showed that some combinations of DAC have additive to synergistic antineoplastic action as compared to DAC alone. The data indicate that combination chemotherapy with DAC merits further investigation. This review may be helpful for the future design of clinical trials using DAC in combination for cancer therapy.

  13. Immunogenicity and protective efficacy study using combination of four tuberculosis DNA vaccines

    Institute of Scientific and Technical Information of China (English)

    蔡宏; 田霞; 呼西旦; 潘怡; 李国利; 庄玉辉; 朱玉贤


    Immune response and protective efficacy for the combination of four tuberculosis DNA vaccines were evaluated in this study. We obtained 1:200 antibody titers against Ag85B 21d after mice were vaccinated for the first time by four recombinant eukaryotic expression vectors containing coding sequences for Ag85B, MPT-64, MPT-63 and ESAT-6. The titers of Ag85B were elevated to 1:102400 after the second injection and decreased to 1:12800 after the third injection. Antibody titers for MPT-64 and MPT-63 reached 1:25600 21 d after the first vaccination, and were then decreased following the second and third injections. No antigen-specific antibody titer against ESAT-6 was detected in sera harvested from immunized mice at any time. These DNA vaccines evoked specific IFN-λ responses in the spleens of vaccinated mice as well. When challenged with M. tuberculosis H37Rv, we found that the lungs of the vaccinated mice produced 99.8% less bacterial counts than that of the empty-vector control group and the bacterial counts were also significantly less than that of the BCG group. Histopathological analyses showed that the lungs of vaccinated mice produced no obvious caseation while over 50%-70% of the pulmonary parenchyma tissue produced central caseation in the vector control group. Our results indicated that the combination of four tuberculosis DNA vaccines may generate high levels of immune responses and result in better animal protection.

  14. Inhibitors of DNA Methylation, Histone Deacetylation, and Histone Demethylation: A Perfect Combination for Cancer Therapy. (United States)

    Zahnow, C A; Topper, M; Stone, M; Murray-Stewart, T; Li, H; Baylin, S B; Casero, R A


    Epigenetic silencing and inappropriate activation of gene expression are frequent events during the initiation and progression of cancer. These events involve a complex interplay between the hypermethylation of CpG dinucleotides within gene promoter and enhancer regions, the recruitment of transcriptional corepressors and the deacetylation and/or methylation of histone tails. These epigenetic regulators act in concert to block transcription or interfere with the maintenance of chromatin boundary regions. However, DNA/histone methylation and histone acetylation states are reversible, enzyme-mediated processes and as such, have emerged as promising targets for cancer therapy. This review will focus on the potential benefits and synergistic/additive effects of combining DNA-demethylating agents and histone deacetylase inhibitors or lysine-specific demethylase inhibitors together in epigenetic therapy for solid tumors and will highlight what is known regarding the mechanisms of action that contribute to the antitumor response.

  15. Identification of DNA primase inhibitors via a combined fragment-based and virtual screening (United States)

    Ilic, Stefan; Akabayov, Sabine R.; Arthanari, Haribabu; Wagner, Gerhard; Richardson, Charles C.; Akabayov, Barak


    The structural differences between bacterial and human primases render the former an excellent target for drug design. Here we describe a technique for selecting small molecule inhibitors of the activity of T7 DNA primase, an ideal model for bacterial primases due to their common structural and functional features. Using NMR screening, fragment molecules that bind T7 primase were identified and then exploited in virtual filtration to select larger molecules from the ZINC database. The molecules were docked to the primase active site using the available primase crystal structure and ranked based on their predicted binding energies to identify the best candidates for functional and structural investigations. Biochemical assays revealed that some of the molecules inhibit T7 primase-dependent DNA replication. The binding mechanism was delineated via NMR spectroscopy. Our approach, which combines fragment based and virtual screening, is rapid and cost effective and can be applied to other targets.

  16. GANN: Genetic algorithm neural networks for the detection of conserved combinations of features in DNA

    Directory of Open Access Journals (Sweden)

    Beiko Robert G


    Full Text Available Abstract Background The multitude of motif detection algorithms developed to date have largely focused on the detection of patterns in primary sequence. Since sequence-dependent DNA structure and flexibility may also play a role in protein-DNA interactions, the simultaneous exploration of sequence- and structure-based hypotheses about the composition of binding sites and the ordering of features in a regulatory region should be considered as well. The consideration of structural features requires the development of new detection tools that can deal with data types other than primary sequence. Results GANN (available at is a machine learning tool for the detection of conserved features in DNA. The software suite contains programs to extract different regions of genomic DNA from flat files and convert these sequences to indices that reflect sequence and structural composition or the presence of specific protein binding sites. The machine learning component allows the classification of different types of sequences based on subsamples of these indices, and can identify the best combinations of indices and machine learning architecture for sequence discrimination. Another key feature of GANN is the replicated splitting of data into training and test sets, and the implementation of negative controls. In validation experiments, GANN successfully merged important sequence and structural features to yield good predictive models for synthetic and real regulatory regions. Conclusion GANN is a flexible tool that can search through large sets of sequence and structural feature combinations to identify those that best characterize a set of sequences.

  17. Clinical variability in neurohepatic syndrome due to combined mitochondrial DNA depletion and Gaucher disease

    Directory of Open Access Journals (Sweden)

    Julie Harvengt


    Full Text Available A 1-year-old girl born to consanguineous parents presented with unexplained liver failure, leading to transplantation at 19 months. Subsequent partial splenectomy for persistent cytopenia showed the presence of foamy cells, and Gaucher disease was confirmed by homozygosity for the p.Leu483Pro mutation in the GBA gene. She was treated by enzyme replacement therapy (ERT. Clinical follow-up showed mild developmental delay, strabismus, nystagmus and oculomotor apraxia. Biochemical studies revealed multiple respiratory chain deficiencies and a mosaic pattern of deficient complex IV immunostaining in liver and fibroblast. Molecular analysis identified a mtDNA depletion syndrome due to the homozygous p.Pro98Leu mutation in MPV17. A younger sister unaffected by mtDNA depletion, presented with pancytopenia and hepatosplenomegaly. ERT for Gaucher disease resulted in visceral normalization without any neurological symptom. A third sister, affected by both conditions, had marked developmental delay, strabismus and ophthalmoplegia but no liver cirrhosis. In conclusion, intrafamilal variability occurs in MPV17-related disease. The combined pathological effect of Gaucher and mitochondrial diseases can negatively impact neurological and liver functions and influence the outcome in consanguineous families. The immunocytochemical staining of OXPHOS protein in tissues and cultured cells is a powerful tool revealing mosaic pattern of deficiency pointing to mtDNA-related mitochondrial disorders.

  18. Combined sequencing of mRNA and DNA from human embryonic stem cells. (United States)

    Mertes, Florian; Kuhl, Heiner; Wruck, Wasco; Lehrach, Hans; Adjaye, James


    Combined transcriptome and whole genome sequencing of the same ultra-low input sample down to single cells is a rapidly evolving approach for the analysis of rare cells. Besides stem cells, rare cells originating from tissues like tumor or biopsies, circulating tumor cells and cells from early embryonic development are under investigation. Herein we describe a universal method applicable for the analysis of minute amounts of sample material (150 to 200 cells) derived from sub-colony structures from human embryonic stem cells. The protocol comprises the combined isolation and separate amplification of poly(A) mRNA and whole genome DNA followed by next generation sequencing. Here we present a detailed description of the method developed and an overview of the results obtained for RNA and whole genome sequencing of human embryonic stem cells, sequencing data is available in the Gene Expression Omnibus (GEO) database under accession number GSE69471.

  19. Determination of DNA adducts by combining acid-catalyzed hydrolysis and chromatographic analysis of the carcinogen-modified nucleobases. (United States)

    Leung, Elvis M K; Deng, Kailin; Wong, Tin-Yan; Chan, Wan


    The commonly used method of analyzing carcinogen-induced DNA adducts involves the hydrolysis of carcinogen-modified DNA samples by using a mixture of enzymes, followed by (32)P-postlabeling or liquid chromatography (LC)-based analyses of carcinogen-modified mononucleotides/nucleosides. In the present study, we report the development and application of a new approach to DNA adduct analysis by combining the H(+)/heat-catalyzed release of carcinogen-modified nucleobases and the use of LC-based methods to analyze DNA adducts. Results showed that heating the carcinogen-modified DNA samples at 70 °C for an extended period of 4 to 6 h in the presence of 0.05% HCl can efficiently induce DNA depurination, releasing the intact carcinogen-modified nucleobases for LC analyses. After optimizing the hydrolysis conditions, DNA samples with C8- and N (2) -modified 2'-deoxyguanosine, as well as N (6) -modified 2'-deoxyadenosine, were synthesized by reacting DNA with 1-nitropyrene, acetaldehyde, and aristolochic acids, respectively. These samples were then hydrolyzed, and the released nucleobase adducts were analyzed using LC-based analytical methods. Analysis results demonstrated a dose-dependent release of target DNA adducts from carcinogen-modified DNA samples, indicating that the developed H(+)/heat-catalyzed hydrolysis method was quantitative. Comparative studies with enzymatic digestion method on carcinogen-modified DNA samples revealed that the two hydrolysis methods did not yield systematically different results.

  20. Rapid Salmonella detection using an acoustic wave device combined with the RCA isothermal DNA amplification method

    Directory of Open Access Journals (Sweden)

    Antonis Kordas


    Full Text Available Salmonella enterica serovar Typhimurium is a major foodborne pathogen that causes Salmonellosis, posing a serious threat for public health and economy; thus, the development of fast and sensitive methods is of paramount importance for food quality control and safety management. In the current work, we are presenting a new approach where an isothermal amplification method is combined with an acoustic wave device for the development of a label free assay for bacteria detection. Specifically, our method utilizes a Love wave biosensor based on a Surface Acoustic Wave (SAW device combined with the isothermal Rolling Circle Amplification (RCA method; various protocols were tested regarding the DNA amplification and detection, including off-chip amplification at two different temperatures (30 °C and room temperature followed by acoustic detection and on-chip amplification and detection at room temperature, with the current detection limit being as little as 100 Bacteria Cell Equivalents (BCE/sample. Our acoustic results showed that the acoustic ratio, i.e., the amplitude over phase change observed during DNA binding, provided the only sensitive means for product detection while the measurement of amplitude or phase alone could not discriminate positive from negative samples. The method's fast analysis time together with other inherent advantages i.e., portability, potential for multi-analysis, lower sample volumes and reduced power consumption, hold great promise for employing the developed assay in a Lab on Chip (LoC platform for the integrated analysis of Salmonella in food samples.

  1. Combining a Ru(II) "Building Block" and Rapid Screening Approach to Identify DNA Structure-Selective "Light Switch" Compounds. (United States)

    Wachter, Erin; Moyá, Diego; Glazer, Edith C


    A chemically reactive Ru(II) "building block", able to undergo condensation reactions with substituted diamines, was utilized to create a small library of luminescent "light switch" dipyrido-[3,2-a:2',3'-c] phenazine (dppz) complexes. The impact of substituent identity, position, and the number of substituents on the light switch effect was investigated. An unbiased, parallel screening approach was used to evaluate the selectivity of the compounds for a variety of different biomolecules, including protein, nucleosides, single stranded DNA, duplex DNA, triplex DNA, and G-quadruplex DNA. Combining these two approaches allowed for the identification of hit molecules that showed different selectivities for biologically relevant DNA structures, particularly triplex and quadruplex DNA.


    Directory of Open Access Journals (Sweden)

    M.W. CHASE


    Full Text Available Iridaceae are one of the largest families of Lilianae and probably also among the best studied families of monocotyledons. To further evaluate generic, tribal and subfamilial relationships, we have produced four plastid DNA data sets for 57 genera of Iridaceae plus outgroups: rps4, rbcL (both protein coding genes, and the trnL intron snd the trnL-F inter-gene spacer. All four matrices produce highly congruent, although not identical trees, and we thus analysed them in a combined analysis, which produced a highly resolved and well supported topology. In each of the individual trees, some genera or groups of genera are misplaced relative to Goldblatt’s and Rudall’s morphological cladistic studies, but the combined analysis produced a pattern much more similar to these previous ideas of relationships. In the combined tree, all subfamilies were resolved as monophyletic clades, except Nivenioideae, which formed a grade in which Ixioideae were embedded. The achlorophyllous Geosiris (sometimes referred to Geosiridaceae or Burmanniaceae fell within the nivenioid grade. Most of the tribes are monophyletic, except for Ixieae, Watsonieae and Sisyrinchieae, but the topology within Ixioideae is not strongly supported due to extremely low levels of sequence divergence. Isophysis is sister to the rest of the family, and Diplarrhena falls in a well supported position as sister to Irideae/Sisyrinchieae/Tigridieae/Mariceae; Bobartia of Sisyrinchieae is supported as a member of Irideae.


    Institute of Scientific and Technical Information of China (English)


    Objective: To clone the human counterpart of rat ZA73, EST cloned from rat tracheal epithelial (RTE) neoplastic transformed cell model induced by (a-particles radiation by using mRNA differential display. Methods: According to the sequence of rat ZA73, a probe was biotin-labeled to screen human cDNA library, and then the gene sequence was extended by RACE (rapid amplification of cDNA ends). Result: Human gene HRNT-1 (GenBank Accession Number: AF223393) is 4.256 kb in length, with an ORF located in the region between 254 and 3013 bp. 5' UTS (untranslated sequences) is 253 bp, 3' UTS is 1243 bp. Conclusion: The combination of cDNA library screening with biotin-labeled probes and RACE is an effective method to clone full-length cDNA, especially for sequences longer than 2 kb.

  4. Analysis of mitochondrial DNA sequences in patients with isolated or combined oxidative phosphorylation system deficiency.

    NARCIS (Netherlands)

    Hinttala, R.; Smeets, R.; Moilanen, J.S.; Ugalde, C.; Uusimaa, J.; Smeitink, J.A.M.; Majamaa, K.


    BACKGROUND: Enzyme deficiencies of the oxidative phosphorylation (OXPHOS) system may be caused by mutations in the mitochondrial DNA (mtDNA) or in the nuclear DNA. OBJECTIVE: To analyse the sequences of the mtDNA coding region in 25 patients with OXPHOS system deficiency to identify the underlying g

  5. Prediction of nucleosome DNA formation potential and nucleosome positioning using increment of diversity combined with quadratic discriminant analysis. (United States)

    Zhao, Xiujuan; Pei, Zhiyong; Liu, Jia; Qin, Sheng; Cai, Lu


    In this work, a novel method was developed to distinguish nucleosome DNA and linker DNA based on increment of diversity combined with quadratic discriminant analysis (IDQD), using k-mer frequency of nucleotides in genome. When used to predict DNA potential for forming nucleosomes, the model achieved a high accuracy of 94.94%, 77.60%, and 86.81%, respectively, for Saccharomyces cerevisiae, Homo sapiens, and Drosophila melanogaster. The area under the receiver operator characteristics curve of our classifier was 0.982 for S. cerevisiae. Our results indicate that DNA sequence preference is critical for nucleosome formation potential and is likely conserved across eukaryotes. The model successfully identified nucleosome-enriched or nucleosome-depleted regions in S. cerevisiae genome, suggesting nucleosome positioning depends on DNA sequence preference. Thus, IDQD classifier is useful for predicting nucleosome positioning.

  6. Combination of native and denaturing PAGE for the detection of protein binding regions in long fragments of genomic DNA

    Directory of Open Access Journals (Sweden)

    Metsis Madis


    Full Text Available Abstract Background In a traditional electrophoresis mobility shift assay (EMSA a 32P-labeled double-stranded DNA oligonucleotide or a restriction fragment bound to a protein is separated from the unbound DNA by polyacrylamide gel electrophoresis (PAGE in nondenaturing conditions. An extension of this method uses the large population of fragments derived from long genomic regions (approximately 600 kb for the identification of fragments containing protein binding regions. With this method, genomic DNA is fragmented by restriction enzymes, fragments are amplified by PCR, radiolabeled, incubated with nuclear proteins and the resulting DNA-protein complexes are separated by two-dimensional PAGE. Shifted DNA fragments containing protein binding sites are identified by using additional procedures, i. e. gel elution, PCR amplification, cloning and sequencing. Although the method allows simultaneous analysis of a large population of fragments, it is relatively laborious and can be used to detect only high affinity protein binding sites. Here we propose an alternative and straightforward strategy which is based on a combination of native and denaturing PAGE. This strategy allows the identification of DNA fragments containing low as well as high affinity protein binding regions, derived from genomic DNA ( Results We have combined an EMSA-based selection step with subsequent denaturing PAGE for the localization of protein binding regions in long (up to10 kb fragments of genomic DNA. Our strategy consists of the following steps: digestion of genomic DNA with a 4-cutter restriction enzyme (AluI, BsuRI, TruI, etc, separation of low and high molecular weight fractions of resultant DNA fragments, 32P-labeling with Klenow polymerase, traditional EMSA, gel elution and identification of the shifted bands (or smear by denaturing PAGE. The identification of DNA fragments containing protein binding sites is carried out by running the gel-eluted fragments alongside

  7. Exogenous DNA internalisation by sperm cells is improved by combining lipofection and restriction enzyme mediated integration. (United States)

    Churchil, R R; Gupta, J; Singh, A; Sharma, D


    1. Three types of exogenous DNA inserts, i.e. complete linearised pVIVO2-GFP/LacZ vector (9620 bp), the LacZ gene (5317 bp) and the GFP gene (2152 bp) were used to transfect chicken spermatozoa through simple incubation of sperm cells with insert. 2. PCR assay, Dot Blot hybridisation and Southern hybridisation showed the successful internalisation of exogenous DNA by chicken sperm cells. 3. Lipofection and Restriction Enzyme Mediated Integration (REMI) were used to improve the rate of internalisation of exogenous DNA by sperm cells. 4. Results from dot blot as well as Southern hybridisation were semi-quantified and improved exogenous DNA uptake by sperm cells through lipofection and REMI. Stronger signals were observed from hybridisation of LacZ as well as GFP specific probe with the DNA from lipofected exogenous DNA transfected sperm DNA in comparison with those transfected with nude exogenous DNA.

  8. Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons

    Directory of Open Access Journals (Sweden)

    De Paepe Anne


    Full Text Available Abstract Background Activation of proto-oncogenes by DNA amplification is an important mechanism in the development and maintenance of cancer cells. Until recently, identification of the targeted genes relied on labour intensive and time consuming positional cloning methods. In this study, we outline a straightforward and efficient strategy for fast and comprehensive cloning of amplified and overexpressed genes. Results As a proof of principle, we analyzed neuroblastoma cell line IMR-32, with at least two amplification sites along the short arm of chromosome 2. In a first step, overexpressed cDNA clones were isolated using a PCR based subtractive cloning method. Subsequent deposition of these clones on a custom microarray and hybridization with IMR-32 DNA, resulted in the identification of clones that were overexpressed due to gene amplification. Using this approach, amplification of all previously reported amplified genes in this cell line was detected. Furthermore, four additional clones were found to be amplified, including the TEM8 gene on 2p13.3, two anonymous transcripts, and a fusion transcript, resulting from 2p13.3 and 2p24.3 fused sequences. Conclusions The combinatorial strategy of subtractive cDNA cloning and array CGH analysis allows comprehensive amplicon dissection, which opens perspectives for improved identification of hitherto unknown targeted oncogenes in cancer cells.

  9. Highly sensitive detection of human IgG using a novel bio-barcode assay combined with DNA chip technology (United States)

    Liu, Zhenbao; Zhou, Bo; Wang, Haiqing; Lu, Feng; Liu, Tianjun; Song, Cunxian; Leng, Xigang


    A simple and ultrasensitive detection of human IgG based on signal amplification using a novel bio-barcode assay and DNA chip technology was developed. The sensing platform was a sandwich system made up of antibody-modified magnetic microparticles (Ab-MMPs)/human IgG/Cy3-labeled single-stranded DNA and antibody-modified gold nanoparticles (Cy3-ssDNA-Ab-AuNPs). The MMPs (2.5 μm in diameter) modified with mouse anti-human IgG monoclonal-antibodies could capture human IgG and further be separated and enriched via a magnetic field. The AuNPs (13 nm in diameter) conjugated with goat anti-human IgG polyclonal-antibodies and Cy3-ssDNA could further combine with the human IgG/Ab-MMP complex. The Cy3-ssDNA on AuNPs was then released by TCEP to hybridize with the DNA chip, thus generating a detectable signal by the fluorescence intensity of Cy3. In order to improve detection sensitivity, a three-level cascaded signal amplification was developed: (1) The MMP enrichment as the first-level; (2) Large quantities of Cy3-ssDNA on AuNPs as the second-level; (3) The Cy3-ssDNA conjugate with DNA chip as the third-level. The highly sensitive technique showed an increased response of the fluorescence intensity to the increased concentration of human IgG through a detection range from 1 pg mL-1 to 10 ng mL-1. This sensing technique could not only improve the detection sensitivity for the low concentration of human IgG but also present a robust and efficient signal amplification model. The detection method has good stability, specificity, and reproducibility and could be applied in the detection of human IgG in the real samples.

  10. Highly sensitive detection of human IgG using a novel bio-barcode assay combined with DNA chip technology

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Zhenbao [Central South University, School of Pharmaceutical Sciences (China); Zhou, Bo, E-mail: [The Affiliated Zhongda Hospital of Southeast University, Department of Gerontology (China); Wang, Haiqing; Lu, Feng; Liu, Tianjun; Song, Cunxian; Leng, Xigang, E-mail: [Institute of Biomedical Engineering, Chinese Academy of Medical Sciences and Peking Union Medical College (China)


    A simple and ultrasensitive detection of human IgG based on signal amplification using a novel bio-barcode assay and DNA chip technology was developed. The sensing platform was a sandwich system made up of antibody-modified magnetic microparticles (Ab-MMPs)/human IgG/Cy3-labeled single-stranded DNA and antibody-modified gold nanoparticles (Cy3-ssDNA-Ab-AuNPs). The MMPs (2.5 {mu}m in diameter) modified with mouse anti-human IgG monoclonal-antibodies could capture human IgG and further be separated and enriched via a magnetic field. The AuNPs (13 nm in diameter) conjugated with goat anti-human IgG polyclonal-antibodies and Cy3-ssDNA could further combine with the human IgG/Ab-MMP complex. The Cy3-ssDNA on AuNPs was then released by TCEP to hybridize with the DNA chip, thus generating a detectable signal by the fluorescence intensity of Cy3. In order to improve detection sensitivity, a three-level cascaded signal amplification was developed: (1) The MMP enrichment as the first-level; (2) Large quantities of Cy3-ssDNA on AuNPs as the second-level; (3) The Cy3-ssDNA conjugate with DNA chip as the third-level. The highly sensitive technique showed an increased response of the fluorescence intensity to the increased concentration of human IgG through a detection range from 1 pg mL{sup -1} to 10 ng mL{sup -1}. This sensing technique could not only improve the detection sensitivity for the low concentration of human IgG but also present a robust and efficient signal amplification model. The detection method has good stability, specificity, and reproducibility and could be applied in the detection of human IgG in the real samples.

  11. Combination of DNA-based and conventional methods to detect human leukocyte antigen polymorphism and its use for paternity testing. (United States)

    Kereszturya, László; Rajczya, Katalin; Lászikb, András; Gyódia, Eva; Pénzes, Mária; Falus, András; Petrányia, Gyõzõ G


    In cases of disputed paternity, the scientific goal is to promote either the exclusion of a falsely accused man or the affiliation of the alleged father. Until now, in addition to anthropologic characteristics, the determination of genetic markers included human leukocyte antigen gene variants; erythrocyte antigens and serum proteins were used for that reason. Recombinant DNA techniques provided a new set of highly variable genetic markers based on DNA nucleotide sequence polymorphism. From the practical standpoint, the application of these techniques to paternity testing provides greater versatility than do conventional genetic marker systems. The use of methods to detect the polymorphism of human leukocyte antigen loci significantly increases the chance of validation of ambiguous results in paternity testing. The outcome of 2384 paternity cases investigated by serologic and/or DNA-based human leukocyte antigen typing was statistically analyzed. Different cases solved by DNA typing are presented involving cases with one or two accused men, exclusions and nonexclusions, and tests of the paternity of a deceased man. The results provide evidence for the advantage of the combined application of various techniques in forensic diagnostics and emphasizes the outstanding possibilities of DNA-based assays. Representative examples demonstrate the strength of combined techniques in paternity testing.

  12. Biochips for cell biology by combined dip-pen nanolithography and DNA-directed protein immobilization. (United States)

    Arrabito, Giuseppe; Reisewitz, Stephanie; Dehmelt, Leif; Bastiaens, Philippe I; Pignataro, Bruno; Schroeder, Hendrik; Niemeyer, Christof M


    A general methodology for patterning of multiple protein ligands with lateral dimensions below those of single cells is described. It employs dip pen nanolithography (DPN) patterning of DNA oligonucleotides which are then used as capture strands for DNA-directed immobilization (DDI) of oligonucleotide-tagged proteins. This study reports the development and optimization of PEG-based liquid ink, used as carrier for the immobilization of alkylamino-labeled DNA oligomers on chemically activated glass surfaces. The resulting DNA arrays have typical spot sizes of 4-5 μm with a pitch of 12 μm micrometer. It is demonstrated that the arrays can be further functionalized with covalent DNA-streptavidin (DNA-STV) conjugates bearing ligands recognized by cells. To this end, biotinylated epidermal growth factor (EGF) is coupled to the DNA-STV conjugates, the resulting constructs are hybridized with the DNA arrays and the resulting surfaces used for the culturing of MCF-7 (human breast adenocarcinoma) cells. Owing to the lateral diffusion of transmembrane proteins in the cell's plasma membrane, specific recruitment and concentration of EGF receptor can be induced specifically at the sites where the ligands are bound on the solid substrate. This is a clear demonstration that this method is suitable for precise functional manipulations of subcellular areas within living cells.

  13. An economical and combined method for rapid and efficient isolation of fungal DNA. (United States)

    Lech, T; Syguła-Cholewinska, J; Szostak-Kot, J


    DNA isolation is a crucial step of conducting genetic studies in any organism. However, this process is quite difficult when studying fungi because of the need to damage the fungal cell walls of specific structures. In this study, we developed a method for the rapid and efficient isolation of fungal DNA based on simultaneous mechanical and enzymatic cell wall degradation. There are several typical modifications of the standard phenol-chloroform DNA extraction method. This method can be modified to degrade the fungal cell wall. The first step of the presented DNA extraction included manual homogenization in modified lysis buffer. Next, enzymatic digestion using 2 enzymes was conducted, including lyticase and proteinase K. To carefully select the most favorable conditions, we developed an economical, rapid, and reliable method for fungal DNA extraction that ensures both high efficiency and proper purity, which are essential for further analyses.

  14. Combining ligation reaction and capillary gel electrophoresis to obtain reliable long DNA probes. (United States)

    García-Cañas, Virginia; Mondello, Monica; Cifuentes, Alejandro


    New DNA amplification methods are continuously developed for sensitive detection and quantification of specific DNA target sequences for, e.g. clinical, environmental or food applications. These new applications often require the use of long DNA oligonucleotides as probes for target sequences hybridization. Depending on the molecular technique, the length of DNA probes ranges from 40 to 450 nucleotides, solid-phase chemical synthesis being the strategy generally used for their production. However, the fidelity of chemical synthesis of DNA decreases for larger DNA probes. Defects in the oligonucleotide sequence result in the loss of hybridization efficiency, affecting the sensitivity and selectivity of the amplification method. In this work, an enzymatic procedure has been developed as an alternative to solid-phase chemical synthesis for the production of long oligonucleotides. The enzymatic procedure for probe production was based on ligation of short DNA sequences. Long DNA probes were obtained from smaller oligonucleotides together with a short sequence that acts as bridge stabilizing the molecular complex for DNA ligation. The ligation reactions were monitored by capillary gel electrophoresis with laser-induced fluorescence detection (CGE-LIF) using a bare fused-silica capillary. The capillary gel electrophoresis-LIF method demonstrated to be very useful and informative for the characterization of the ligation reaction, providing important information about the nature of some impurities, as well as for the fine optimization of the ligation conditions (i.e. ligation cycles, oligonucleotide and enzyme concentration). As a result, the yield and quality of the ligation product were highly improved. The in-lab prepared DNA probes were used in a novel multiplex ligation-dependent genome amplification (MLGA) method for the detection of genetically modified maize in samples. The great possibilities of the whole approach were demonstrated by the specific and sensitive

  15. A strategy of tumor treatment in mice with doxorubicin-cyclophosphamide combination based on dendritic cell activation by human double-stranded DNA preparation


    Alyamkina, Ekaterina A; Nikolin, Valeriy P; Popova, Nelly A.; Dolgova, Evgenia V; Proskurina, Anastasia S; Orishchenko, Konstantin E.; Efremov, Yaroslav R.; Chernykh, Elena R.; Ostanin, Alexandr A.; Sidorov, Sergey V; Ponomarenko, Dmitriy M.; Zagrebelniy, Stanislav N; Bogachev, Sergey S.; Shurdov, Mikhail A


    Background Immunization of mice with tumor homogenate after combined treatment with cyclophosphamide (CP) and double-stranded DNA (dsDNA) preparation is effective at inhibition of growth of tumor challenged after the treatment. It was assumed that this inhibition might be due to activation of the antigen-presenting cells. The purpose was to develop improved antitumor strategy using mice. We studied the combined action of cytostatics doxorubicin (Dox) plus CP with subsequent dsDNA preparation ...

  16. A DNA-based system for selecting and displaying the combined result of two input variables

    DEFF Research Database (Denmark)

    Liu, Huajie; Wang, Jianbang; Song, S


    demonstrate this capability in a DNA-based system that takes two input numbers, represented in DNA strands, and returns the result of their multiplication, writing this as a number in a display. Unlike a conventional calculator, this system operates by selecting the result from a library of solutions rather...... than through logic operations. The multiplicative example demonstrated here illustrates a much more general capability—to generate a unique output for any distinct pair of DNA inputs. The system thereby functions as a lookup table and could be a key component in future, more powerful data......-processing systems for diagnostics and sensing....

  17. Quantification of DNA synthesis in multicellular organisms by a combined DAPI and BrdU technique. (United States)

    Knobloch, Jürgen; Kunz, Werner; Grevelding, Christoph G


    The development of a novel method to detect and quantify mitotic activity in multicellular organisms is reported. The method is based on the combinatorial use of 4',6-diamidino-2-phenylindole (DAPI) as a dye for the specific staining of DNA and the thymidine analog 5-bromo-2'-deoxyuridine (BrdU) as a marker for DNA synthesis. It is shown that on nitrocellulose filters, the amount of DNA can be determined by DAPI as a prerequisite for the subsequent quantification of mitotic activity by BrdU. As a model system to prove the applicability of this technique, the blood fluke Schistosoma mansoni has been used. It is demonstrated that the DNA synthesis rate is higher in adult female schistosomes than in adult males. Furthermore, dimethyl sulfoxide, a widely used solvent for many mitogens and inhibitors of mitosis, has no influence on mitotic activity in adult schistosomes.


    Directory of Open Access Journals (Sweden)

    G. B. Skamrova


    Full Text Available Now the number of physical and chemical biologically active damage factors dramatically increased. The ways to neutralize such effects have not been studied enough. In this work the techniques of visual assessment of chromatin granulation and of electronegativity of human buccal epithelium cell nuclei were used in order to study the combined effects of the exposure to low-intensity electromagnetic radiation of the millimeter range electromagnetic radiation and to the DNA-binding compounds, such as: antibiotic doxorubicin, mutagens ethidium bromide and proflavine, as well as to caffeine and C60 -fullerene which are not directly interact with DNA. When the action of electromagnetic radiation and DNA-binding compounds is combined, a synergistic effect of reducing the cell response was observed in contrast to the effects caused by electromagnetic radiation and drugs separately. When cells were irradiated in the presence of C60 -fullerene or caffeine, a protective effect of compounds against electromagnetic radiation influence was observed. The obtained results may provide perspectives in the use of the C60 fullerene and caffeine as DNA-protectors under the action of electromagnetic radiation.

  19. Combined DNA and lipid analyses of sediments reveal changes in Holocene haptophyte and diatom populations in an Antarctic lake (United States)

    Coolen, Marco J. L.; Muyzer, Gerard; Rijpstra, W. Irene C.; Schouten, Stefan; Volkman, John K.; Sinninghe Damsté, Jaap S.


    Preserved ribosomal DNA of planktonic phototrophic algae was recovered from Holocene anoxic sediments of Ace Lake (Antarctica), and the ancient community members were identified based on comparative sequence analysis. The similar concentration profiles of DNA of haptophytes and their traditional lipid biomarkers (alkenones and alkenoates) revealed that fossil rDNA also served as quantitative biomarkers in this environment. The DNA data clearly revealed the presence of six novel phylotypes related to known alkenone and alkenoate-biosynthesizing haptophytes with Isochrysis galbana UIO 102 as their closest relative. The relative abundance of these phylotypes changed as the lake chemistry, particularly salinity, evolved over time. Changes in the alkenone distributions reflect these population changes rather than a physiological response to salinity by a single haptophyte. Using this novel paleo-ecological approach of combining data from lipid biomarkers and preserved DNA, we showed that the post-glacial development of Ace Lake from freshwater basin to marine inlet and the present-day lacustrine saline system caused major qualitative and quantitative changes in the biodiversity of the planktonic populations over time.

  20. Combined immunity of DNA vector and recombinant vaccinia virus expressing Gag proteins of equine infectious anemia virus

    Institute of Scientific and Technical Information of China (English)

    DAI Chunming; ZHANG Xiaoyan; WANG Shuhui; LIU Ying; DUAN Danli; SHEN Rongxian; SHAO Yiming


    In order to develop a new vaccine candidate for equine infectious anemia virus (EIAV), gag gene of Chinese donkey leukocyte attenuated strain (EIAV DLV) and its parental virulent strain (EIAV LN) were inserted respectively into the TK region of the Tiantan strain (VV) of vaccinia virus by homologous recombination and the positive clone was confirmed by blue plaque assay. Protein expression was examined by Western blot. Prime and prime-boost procedures were used to immunize mice with two DNA vectors and two recombinant vaccinia viruses expressing EIAV Gag proteins. The results showed that the specific lysis of CTL responses in the DNA+rVV groups was stronger than those in the DNA groups, amounting to 31%. Although the levels of specific antibodies were not significantly different, we could conclude that the recombinant vaccinia virus could boost the cellular responses following DNA vector priming. There was no detectable difference between the immune responses induced by DLV and LN Gag proteins. This data demonstrates that the combined immunity of DNA vector and recombinant vaccinia virus expressing EIAV gag proteins, utilizing the prime-boost procedure, can drive immunized mice to produce powerful cellular responses. These results lay an important foundation for the development of a new EIAV genetic engineering vaccine.

  1. Two-photon fluorescence and fluorescence imaging of two styryl heterocyclic dyes combined with DNA. (United States)

    Gao, Chao; Liu, Shu-yao; Zhang, Xian; Liu, Ying-kai; Qiao, Cong-de; Liu, Zhao-e


    Two new styryl heterocyclic two-photon (TP) materials, 4-[4-(N-methyl)styrene]-imidazo [4,5-f][1,10] phenanthroline-benzene iodated salt (probe-1) and 4,4-[4-(N-methyl)styrene]-benzene iodated salt (probe-2) were successfully synthesized and studied as potential fluorescent probes of DNA detection. The linear and nonlinear photophysical properties of two compounds in different solvents were investigated. The absorption, one- and two-photon fluorescent spectra of the free dye and dye-DNA complex were also examined to evaluate their photophysical properties. The binding constants of dye-DNA were obtained according to Scatchard equation with good values. The results showed that two probes could be used as fluorescent DNA probes by two-photon excitation, and TP fluorescent properties of probe-1 are superior to that of probe-2. The fluorescent method date indicated that the mechanisms of dye-DNA complex interaction may be groove binding for probe-1 and electrostatic interaction for probe-2, respectively. The MTT assay experiments showed two probes are low toxicity. Moreover, the TP fluorescence imaging of DNA detection in living cells at 800 nm indicated that the ability to locate in cell nuclei of probe-1 is better than that of probe-2.



    G. B. Skamrova; Prylutskyy, Yu I.; M. P. Evstigneev


    Now the number of physical and chemical biologically active damage factors dramatically increased. The ways to neutralize such effects have not been studied enough. In this work the techniques of visual assessment of chromatin granulation and of electronegativity of human buccal epithelium cell nuclei were used in order to study the combined effects of the exposure to low-intensity electromagnetic radiation of the millimeter range electromagnetic radiation and to the DNA-binding compounds, su...

  3. Microplate-based platform for combined chromatin and DNA methylation immunoprecipitation assays

    Directory of Open Access Journals (Sweden)

    Yu Jingjing


    Full Text Available Abstract Background The processes that compose expression of a given gene are far more complex than previously thought presenting unprecedented conceptual and mechanistic challenges that require development of new tools. Chromatin structure, which is regulated by DNA methylation and histone modification, is at the center of gene regulation. Immunoprecipitations of chromatin (ChIP and methylated DNA (MeDIP represent a major achievement in this area that allow researchers to probe chromatin modifications as well as specific protein-DNA interactions in vivo and to estimate the density of proteins at specific sites genome-wide. Although a critical component of chromatin structure, DNA methylation has often been studied independently of other chromatin events and transcription. Results To allow simultaneous measurements of DNA methylation with other genomic processes, we developed and validated a simple and easy-to-use high throughput microplate-based platform for analysis of DNA methylation. Compared to the traditional beads-based MeDIP the microplate MeDIP was more sensitive and had lower non-specific binding. We integrated the MeDIP method with a microplate ChIP assay which allows measurements of both DNA methylation and histone marks at the same time, Matrix ChIP-MeDIP platform. We illustrated several applications of this platform to relate DNA methylation, with chromatin and transcription events at selected genes in cultured cells, human cancer and in a model of diabetic kidney disease. Conclusion The high throughput capacity of Matrix ChIP-MeDIP to profile tens and potentially hundreds of different genomic events at the same time as DNA methylation represents a powerful platform to explore complex genomic mechanism at selected genes in cultured cells and in whole tissues. In this regard, Matrix ChIP-MeDIP should be useful to complement genome-wide studies where the rich chromatin and transcription database resources provide fruitful foundation

  4. Combining SSH and cDNA microarrays for rapid identification of differentially expressed genes. (United States)

    Yang, G P; Ross, D T; Kuang, W W; Brown, P O; Weigel, R J


    Comparing patterns of gene expression in cell lines and tissues has important applications in a variety of biological systems. In this study we have examined whether the emerging technology of cDNA microarrays will allow a high throughput analysis of expression of cDNA clones generated by suppression subtractive hybridization (SSH). A set of cDNA clones including 332 SSH inserts amplified by PCR was arrayed using robotic printing. The cDNA arrays were hybridized with fluorescent labeled probes prepared from RNA from ER-positive (MCF7 and T47D) and ER-negative (MDA-MB-231 and HBL-100) breast cancer cell lines. Ten clones were identified that were over-expressed by at least a factor of five in the ER-positive cell lines. Northern blot analysis confirmed over-expression of these 10 cDNAs. Sequence analysis identified four of these clones as cytokeratin 19, GATA-3, CD24 and glutathione-S-transferase mu-3. Of the remaining six cDNA clones, four clones matched EST sequences from two different genes and two clones were novel sequences. Flow cytometry and immunofluorescence confirmed that CD24 protein was over-expressed in the ER-positive cell lines. We conclude that SSH and microarray technology can be successfully applied to identify differentially expressed genes. This approach allowed the identification of differentially expressed genes without the need to obtain previously cloned cDNAs.

  5. Combined RNA/DNA fluorescence in situ hybridization on whole-mount Drosophila ovaries. (United States)

    Shpiz, Sergey; Lavrov, Sergey; Kalmykova, Alla


    DNA FISH (fluorescent in situ hybridization) analysis reveals the chromosomal location of the gene of interest. RNA in situ hybridization is used to examine the amounts and cell location of transcripts. This method is commonly used to describe the localization of processed transcripts in different tissues or cell lines. Gene activation studies are often aimed at determining the mechanism of this activation (transcriptional or posttranscriptional). Elucidation of the mechanism of piRNA-mediated silencing of genomic repeats is at the cutting edge of small RNA research. The RNA/DNA FISH technique is a powerful method for assessing transcriptional changes at any particular genomic locus. Colocalization of the RNA and DNA FISH signals allows a determination of the accumulation of nascent transcripts at the transcribed genomic locus. This would be suggest that this gene is activated at the transcriptional (or co-transcriptional) level. Moreover, this method allows for the identification of transcriptional derepression of a distinct copy (copies) among a genomic repeat family. Here, a RNA/DNA FISH protocol is presented for the simultaneous detection of RNA and DNA in situ on whole-mount Drosophila ovaries using tyramide signal amplification. With subsequent immunostaining of chromatin components, this protocol can be easily extended for studying the interdependence between chromatin changes at genomic loci and their transcriptional activity.

  6. Combining Electro-Osmotic Flow and FTA® Paper for DNA Analysis on Microfluidic Devices

    Directory of Open Access Journals (Sweden)

    Ryan Wimbles


    Full Text Available FTA® paper can be used to protect a variety of biological samples prior to analysis, facilitating ease-of-transport to laboratories or long-term archive storage. The use of FTA® paper as a solid phase eradicates the need to elute the nucleic acids from the matrix prior to DNA amplification, enabling both DNA purification and polymerase chain reaction (PCR-based DNA amplification to be performed in a single chamber on the microfluidic device. A disc of FTA® paper, containing a biological sample, was placed within the microfluidic device on top of wax-encapsulated DNA amplification reagents. The disc containing the biological sample was then cleaned up using Tris-EDTA (TE buffer, which was passed over the disc, via electro-osmotic flow, in order to remove any potential inhibitors of downstream processes. DNA amplification was successfully performed (from buccal cells, whole blood and semen using a Peltier thermal cycling system, whereupon the stored PCR reagents were released during the initial denaturing step due to the wax barrier melting between the FTA® disc and PCR reagents. Such a system offers advantages in terms of a simple sample introduction interface and the ability to process archived samples in an integrated microfluidic environment with minimal risk of contamination.

  7. Detection of Genetically Modified Crops by Combination of Multiplex PCR and Low-density DNA Microarray1

    Institute of Scientific and Technical Information of China (English)



    Objective To develop a technique for simultaneous detection of various target genes in Roundup Ready soybean by combining multiplex PCR and low-density DNA microarray.Methods Two sets of the multiplex PCR system were used to amplify the target genes in genetically modified(GM)soybean.Seventeen capture probes(PCR products)and 17 pairs of corresponding primers were designed according to the genetic characteristies of Rroundup Ready soybean(GTS40-3-2),maize (Mort810,Nk603,GA21),canola(T45,MS1/RF1),and rice(SCK)in many identified GM crops.All of the probes were categorized and identified as species-specific probes.One negative probe and one positive control probe were uscd to assess the efficiency of all reactions,and therefore eliminate any false positive and negative results.After multiplex PCR reaction,amplicons were adulterated with Cy5-dUTP and hvbridized with DNA microarray.The array was then scanned to display the specific hybridization signals of target genes.The assay was applied to the analysis of sample of ccrtified transgenic soybean (Roundup Ready GTS40-3-2)and canola(MS1/RF1). Results A combination technique of multiplex PCR and DNA microarray was successfully developed to identify multi-target genes in Roundup Ready soybean and MS1/RF1 canola with a great specificity and reliability.Reliable identification of genetic characteristics of Roundup Ready of GM soybean from genetically modified crops was achieved at 0.5% transgenic events,indicating a high sensitivity. Conclusion A combination technique of multiplex PCR and low-density DNA microarray can reliably detect and identify the genetically modified crops.

  8. Combination of gefitinib and DNA methylation inhibitor decitabine exerts synergistic anti-cancer activity in colon cancer cells.

    Directory of Open Access Journals (Sweden)

    Yun-feng Lou

    Full Text Available Despite recent advances in the treatment of human colon cancer, the chemotherapy efficacy against colon cancer is still unsatisfactory. In the present study, effects of concomitant inhibition of the epidermal growth factor receptor (EGFR and DNA methyltransferase were examined in human colon cancer cells. We demonstrated that decitabine (a DNA methyltransferase inhibitor synergized with gefitinib (an EGFR inhibitor to reduce cell viability and colony formation in SW1116 and LOVO cells. However, the combination of the two compounds displayed minimal toxicity to NCM460 cells, a normal human colon mucosal epithelial cell line. The combination was also more effective at inhibiting the AKT/mTOR/S6 kinase pathway. In addition, the combination of decitabine with gefitinib markedly inhibited colon cancer cell migration. Furthermore, gefitinib synergistically enhanced decitabine-induced cytotoxicity was primarily due to apoptosis as shown by Annexin V labeling that was attenuated by z-VAD-fmk, a pan caspase inhibitor. Concomitantly, cell apoptosis resulting from the co-treatment of gefitinib and decitabine was accompanied by induction of BAX, cleaved caspase 3 and cleaved PARP, along with reduction of Bcl-2 compared to treatment with either drug alone. Interestingly, combined treatment with these two drugs increased the expression of XIAP-associated factor 1 (XAF1 which play an important role in cell apoptosis. Moreover, small interfering RNA (siRNA depletion of XAF1 significantly attenuated colon cancer cells apoptosis induced by the combination of the two drugs. Our findings suggested that gefitinib in combination with decitabine exerted enhanced cell apoptosis in colon cancer cells were involved in mitochondrial-mediated pathway and induction of XAF1 expression. In conclusion, based on the observations from our study, we suggested that the combined administration of these two drugs might be considered as a novel therapeutic regimen for treating colon

  9. Global eukaryote phylogeny: Combined small- and large-subunit ribosomal DNA trees support monophyly of Rhizaria, Retaria and Excavata. (United States)

    Moreira, David; von der Heyden, Sophie; Bass, David; López-García, Purificación; Chao, Ema; Cavalier-Smith, Thomas


    Resolution of the phylogenetic relationships among the major eukaryotic groups is one of the most important problems in evolutionary biology that is still only partially solved. This task was initially addressed using a single marker, the small-subunit ribosomal DNA (SSU rDNA), although in recent years it has been shown that it does not contain enough phylogenetic information to robustly resolve global eukaryotic phylogeny. This has prompted the use of multi-gene analyses, especially in the form of long concatenations of numerous conserved protein sequences. However, this approach is severely limited by the small number of taxa for which such a large number of protein sequences is available today. We have explored the alternative approach of using only two markers but a large taxonomic sampling, by analysing a combination of SSU and large-subunit (LSU) rDNA sequences. This strategy allows also the incorporation of sequences from non-cultivated protists, e.g., Radiozoa (=radiolaria minus Phaeodarea). We provide the first LSU rRNA sequences for Heliozoa, Apusozoa (both Apusomonadida and Ancyromonadida), Cercozoa and Radiozoa. Our Bayesian and maximum likelihood analyses for 91 eukaryotic combined SSU+LSU sequences yielded much stronger support than hitherto for the supergroup Rhizaria (Cercozoa plus Radiozoa plus Foraminifera) and several well-recognised groups and also for other problematic clades, such as the Retaria (Radiozoa plus Foraminifera) and, with more moderate support, the Excavata. Within opisthokonts, the combined tree strongly confirms that the filose amoebae Nuclearia are sisters to Fungi whereas other Choanozoa are sisters to animals. The position of some bikont taxa, notably Heliozoa and Apusozoa, remains unresolved. However, our combined trees suggest a more deeply diverging position for Ancyromonas, and perhaps also Apusomonas, than for other bikonts, suggesting that apusozoan zooflagellates may be central for understanding the early evolution of


    Directory of Open Access Journals (Sweden)

    M. A. M. Inggas


    Full Text Available Background: Glioblastoma multiforme (GBM is the most aggressive primary brain tumor in adultswith dismal prognosis due to the unavailability of an effective therapy. Up to now, there had been no definitive studies published on EGFR inhibition therapy as a chemosensitizer for GBM therapy using Temozolomide (TMZ. This study aims to reveal the most effective method and timing to administer TMZ-anti EGFR targeted therapy which causes maximal DNA damage on GBM cells.Methods: Various regimens of anti EGFR monoclonal antibody Nimotuzumab (NMZ was administered in different combinations with TMZ, performed on U87MG MGMT(+ EGFR(+ cells. The effectiveness of the combinations were evaluated by measuring yH2AX levels which reflects the degree of DNA damage. One-way Anova and LSD tests were performed to determine the effects of each treatment with p<0.05. Results and discussion: the mean SD of yH2AX of each treatment was: 11,90±1,25 for the control group; 29.33±1.91 for NMZ alone; 28.13±1.58 for TMZ alone; 41.53±3.51 for concurrent use; 35.67 ±2.65 for NMZ after 24 hours TMZ; 31.87±2.94 for NMZ after 48 hours TMZ; 39.57±4.2 for TMZ after 24 hours NMZ; and 35.93 ±3.56 for TMZ after 48 hours NMZ. The administration of TMZ concurrent with or after 24 hours NMZ gives the highest amount of DNA damage to GBM cells. Conclusion: The administration of Nimotuzumab targeted therapy up to 24 hours before Temozolomide chemotherapy has been proven to be effective in maximizing the amount of DNA damage done to GBM cells in vitro. 

  11. DNA bases assembled on the Au(110)/electrolyte interface: A combined experimental and theoretical study

    DEFF Research Database (Denmark)

    Salvatore, Princia; Nazmutdinov, Renat R.; Ulstrup, Jens;


    of the adlayers of the four DNA bases by EC-STM disclosed lifting of the Au(110) reconstruction, specific molecular packing in dense monolayers, and pH dependence of the A and G adsorption. DFT computations based on a cluster model for the Au(110) surface were performed to investigate the adsorption energy......Among the low-index single-crystal gold surfaces, the Au(110) surface is the most active toward molecular adsorption and the one with fewest electrochemical adsorption data reported. Cyclic voltammetry (CV), electrochemically controlled scanning tunneling microscopy (EC-STM), and density functional......, accompanied by a pair of strong voltammetry peaks in the double-layer region in acid solutions. Adsorption of the DNA bases gives featureless voltammograms with lower double-layer capacitance, suggesting that all the bases are chemisorbed on the Au(110) surface. Further investigation of the surface structures...

  12. A novel method to perform genomic walks using a combination of single strand DNA circularization and rolling circle amplification. (United States)

    Gadkar, Vijay J; Filion, Martin


    Characterization of regions flanking a known sequence within a genome, known as genome walking, is a cornerstone technique in modern genetic analysis. In the present work we have developed a new PCR-dependent, directional genome walking protocol based on the unique circularization property of a novel DNA ligase, CircLigase. In the first step, PCR based primer extension is performed using a phosphorylated primer, designed to extend from the boundary of the known sequence, into the flanking region. This linear amplification results in the generation of single-stranded (ss) DNA, which is then circularized using CircLigase. Using the hyperbranching activity of Phi29 DNA polymerase, the circular ssDNA is then linearized by rolling circle amplification, resulting in copious amounts of double stranded concatameric DNA. Nested primers are used to amplify the flanking sequence using inverse PCR. The products are resolved on an agarose gel and the bands whose mobility change due to the nested location of the primer combination used are identified, extracted, and cloned into a plasmid vector for sequencing. Empirical proof for this concept was generated on two antimicrobial biosynthetic genes in Pseudomonas sp. LBUM300. Using the hcnB and phlD genes as starting points, ca 1 kb of flanking sequences were successfully isolated. The use of locus specific primers ensured both directionality and specificity of the walks, alleviating the generation of spurious amplicons, typically observed in randomly primed walking protocols. The presented genome walking protocol could be applied to any microbial genome and requires only 100-150 bp of prior sequence information. The proposed methodology does not entail laborious testing of restriction enzymes or adaptor ligation. This is the first report of a successful application of the novel ligase enzyme, CircLigase for genomic walking purposes.

  13. Mitochondrial DNA deletion in a patient with combined features of Leigh and Pearson syndromes

    Energy Technology Data Exchange (ETDEWEB)

    Blok, R.B.; Thorburn, D.R.; Danks, D.M. [Royal Children`s Hospital, Melbourne (Australia)] [and others


    We describe a heteroplasmic 4237 bp mitochondrial DNA (mtDNA) deletion in an 11 year old girl who has suffered from progressive illness since birth. She has some features of Leigh syndrome (global developmental delay with regression, brainstem dysfunction and lactic acidosis), together with other features suggestive of Pearson syndrome (history of pancytopenia and failure to thrive). The deletion was present at a level greater than 50% in skeletal muscle, but barely detectable in skin fibroblasts following Southern blot analysis, and only observed in blood following PCR analysis. The deletion spanned nt 9498 to nt 13734, and was flanked by a 12 bp direct repeat. Genes for cytochrome c oxidase subunit III, NADH dehydrogenase subunits 3, 4L, 4 and 5, and tRNAs for glycine, arginine, histidine, serine({sup AGY}) and leucine({sup CUN}) were deleted. Southern blotting also revealed an altered Apa I restriction site which was shown by sequence analysis to be caused by G{r_arrow}A nucleotide substitution at nt 1462 in the 12S rRNA gene. This was presumed to be a polymorphism. No abnormalities of mitochondrial ultrastructure, distribution or of respiratory chain enzyme complexes I-IV in skeletal muscle were observed. Mitochondrial disorders with clinical features overlapping more than one syndrome have been reported previously. This case further demonstrates the difficulty in correlating observed clinical features with a specific mitochondrial DNA mutation.

  14. Rapid detection of hepatitis B virus DNA in liver tissue by in situ hybridisation and its combination with immunohistochemistry for simultaneous detection of HBV antigens.


    Lau, J. Y.; Naoumov, N V; Alexander, G J; Williams, R


    A rapid technique using a non-radioactive receptor molecule (digoxigenin) for intrahepatic hepatitis B virus (HBV) DNA detection using in situ hybridisation was developed. It can be adapted for use in combination with standard immunohistochemistry for simultaneous detection of both HBV DNA and HBV antigens. The total time required for dual detection of HBV antigens and HBV DNA starting from paraffin wax liver sections was two working days. A good signal to background ratio for the detection o...

  15. Construction of two fluorescence-labeled non-combined DNA index system miniSTR multiplex systems to analyze degraded DNA samples in the Chinese Han Population. (United States)

    Bai, Xue; Li, Shujin; Cong, Bin; Li, Xia; Guo, Xia; He, Lujun; Ye, Jian; Pei, Li


    MiniSTR loci have been demonstrated to be an effective approach in recovering genetic information from degraded specimens, because of the reduced PCR amplicon sizes which improved the PCR efficiency. Eight non-combined DNA index system miniSTR loci suitable for the Chinese Han Population were analyzed in 300 unrelated Chinese Han individuals using two novel five fluorescence-labeled miniSTR multiplex systems(multiplex I: D10S1248, D2S441, D1S1677 and D9S2157; multiplex II: D9S1122, D10S1435, D12ATA63, D2S1776 and Amelogenin). The allele frequency distribution and forensic parameters in the Chinese Han Population were reported in this article. The Exact Test demonstrated that all loci surveyed here were found to be no deviation from Hardy-Weinberg equilibrium. The accumulated power of discrimination and power of exclusion for the eight loci were 0.999999992 and 0.98, respectively. The highly degraded DNA from artificially degraded samples and the degraded forensic case work samples was assessed with the two miniSTR multiplex systems, and the results showed that the systems were quite effective.

  16. Combination of cascade chemical reactions with graphene-DNA interaction to develop new strategy for biosensor fabrication. (United States)

    Zhu, Xiaoli; Sun, Liya; Chen, Yangyang; Ye, Zonghuang; Shen, Zhongming; Li, Genxi


    Graphene, a single atom thick and two dimensional carbon nano-material, has been proven to possess many unique properties, one of which is the recent discovery that it can interact with single-stranded DNA through noncovalent π-π stacking. In this work, we demonstrate that a new strategy to fabricate many kinds of biosensors can be developed by combining this property with cascade chemical reactions. Taking the fabrication of glucose sensor as an example, while the detection target, glucose, may regulate the graphene-DNA interaction through three cascade chemical reactions, electrochemical techniques are employed to detect the target-regulated graphene-DNA interaction. Experimental results show that in a range from 5μM to 20mM, the glucose concentration is in a natural logarithm with the logarithm of the amperometric response, suggesting a best detection limit and detection range. The proposed biosensor also shows favorable selectivity, and it has the advantage of no need for labeling. What is more, by controlling the cascade chemical reactions, detection of a variety of other targets may be achieved, thus the strategy proposed in this work may have a wide application potential in the future.

  17. Combining peptide and DNA for protein assay: CRIP1 detection for breast cancer staging. (United States)

    Xie, Haona; Li, Hao; Huang, Yue; Wang, Xiaoying; Yin, Yongmei; Li, Genxi


    In this work, a novel method for a protein assay is proposed which uses the specific protein-binding peptide of the target protein and sequence-specific DNA to interact with the target as the capture and detection probe, respectively. Meanwhile, since the DNA sequence can be coupled with gold nanoparticles to amplify the signal readout, a sensitive and easily operated method for protein assay is developed. We have also employed a transcription factor named as cysteine-rich intestinal protein 1 (CRIP1), which has been identified as an ideal biomarker for staging of breast cancer, as the model protein for this study. With the proposed method, CRIP1 can be determined in a linear range from 1.25 to 10.13 ng/mL, with a detection limit of 1.25 ng/mL. Furthermore, the proposed method can be directly used to assay CRIP1 in tissue samples. Owing to its desirable sensitivity, excellent reproducibility, and high selectivity, the proposed method may hold great potential in clinical practice in the future.

  18. Effects of combined immune therapy on survival and Th1/rh2 cytokine balance in rat orthotopic liver transplantation

    Institute of Scientific and Technical Information of China (English)

    CAO Hui; LIU Hua; WU Zhi-yong


    Background The induction of immune tolerance and suppression of allograft rejection has become the focus in the study of liver transplantation. The effect of immune therapy with anti-CD40L mAb alone or in combination with cyclosporine A (CsA) on the recipient survival and Th1/Th2 cytokine profile was studied to elucidate its immunological mechanism and role in rat orthotopic liver transplantation.Methods The model of rat orthotopic liver transplantation was established by modified Kamada's technique.Recipients were divided into group A (control group): SD→SD; group B (group of rejection): SD→Wistar without any treatment; group C: SD→Wistar with CsA monotherapy from day 1 to day 5; and group D: SD→Wistar with CsA from day 1 to day 5 and anti-CD40L mAb on day 0 and day 2. The survival of the recipients in all groups was observed and ELISA technique was used to detect the level of cytokines in peripheral blood on post-transplant day 7.Results The survival period of recipients in groups A (>60 days) and D (>60 days) was significantly longer than that in group B (13.8±2.4 days). The serum levels of interleukin 2 (IL-2) and interferon y in group B were significantly higher than those in other groups; the level of tumor necrosis factor α was higher but not statistically significant. In contrast, the serum levels of IL-4 and IL-10 in group D were elevated more significantly than those in group B (P<0.05).Conclusions Combined immune therapy can prolong the survival of allografts. Increased expression of Th2 cytokines, which is closely related to the induction of tolerance and suppression of rejection, is beneficial to the long-term survival of recipients and allografts.

  19. Combined DNA, toxicological and heavy metal analyses provides an auditing toolkit to improve pharmacovigilance of traditional Chinese medicine (TCM) (United States)

    Coghlan, Megan L.; Maker, Garth; Crighton, Elly; Haile, James; Murray, Dáithí C.; White, Nicole E.; Byard, Roger W.; Bellgard, Matthew I.; Mullaney, Ian; Trengove, Robert; Allcock, Richard J. N.; Nash, Christine; Hoban, Claire; Jarrett, Kevin; Edwards, Ross; Musgrave, Ian F.; Bunce, Michael


    Globally, there has been an increase in the use of herbal remedies including traditional Chinese medicine (TCM). There is a perception that products are natural, safe and effectively regulated, however, regulatory agencies are hampered by a lack of a toolkit to audit ingredient lists, adulterants and constituent active compounds. Here, for the first time, a multidisciplinary approach to assessing the molecular content of 26 TCMs is described. Next generation DNA sequencing is combined with toxicological and heavy metal screening by separation techniques and mass spectrometry (MS) to provide a comprehensive audit. Genetic analysis revealed that 50% of samples contained DNA of undeclared plant or animal taxa, including an endangered species of Panthera (snow leopard). In 50% of the TCMs, an undeclared pharmaceutical agent was detected including warfarin, dexamethasone, diclofenac, cyproheptadine and paracetamol. Mass spectrometry revealed heavy metals including arsenic, lead and cadmium, one with a level of arsenic >10 times the acceptable limit. The study showed 92% of the TCMs examined were found to have some form of contamination and/or substitution. This study demonstrates that a combination of molecular methodologies can provide an effective means by which to audit complementary and alternative medicines.

  20. Venom landscapes: mining the complexity of spider venoms via a combined cDNA and mass spectrometric approach. (United States)

    Escoubas, Pierre; Sollod, Brianna; King, Glenn F


    The complexity of Australian funnel-web spider venoms has been explored via the combined use of MALDI-TOF mass spectrometry coupled with chromatographic separation and the analysis of venom-gland cDNA libraries. The results show that these venoms are far more complex than previously realized. We show that the venoms of Australian funnel-web spiders contain many hundreds of peptides that follow a bimodal distribution, with about 75% of the peptides having a mass of 3000-5000 Da. The mass spectral data were validated by matching the experimentally observed masses with those predicted from peptide sequences derived from analysis of venom-gland cDNA libraries. We show that multiple isoforms of these peptides are found in small chromatographic windows, which suggests that the wide distribution of close molecular weights among the chromatographic fractions probably reflects a diversity of structures and physicochemical properties. The combination of all predicted and measured parameters permits the interpretation of three-dimensional 'venom landscapes' derived from LC-MALDI analysis. We propose that these venom landscapes might have predictive value for the discovery of various groups of pharmacologically distinct toxins in complex venoms.

  1. Study on the Detection of Telomerase Activity by Combining DNA Sequence Analysis with TRAP

    Institute of Scientific and Technical Information of China (English)


    Telomeric repeat amplification protocol (TRAP) is now aconventional assay for detecting telomerase activity. However, this method presents problems owing to tedious quantitation, radioisotopic handling. In order to alleviate these inconveniences, a novel telomerase DNA sequencing assay together with TRAP to detect human telomerase activity was developed. It was used to detect telomerase activity in Hela, HLF, MCF, K562, SMMC-7721 cells, Leukocytes and RNase-pretreated or heat-treated cells as control. Telomerase activity assayed by this method was positive when the number of K562 cells examined was 102,103, and 104. The telomerase activity depended on the number of K562 cells used in the assay. Telomerase activity of Rnase-pretreated cells or heat-treated cells, and human normal peripheral blood leukocyte(Leu) were negative. The result of this method was available within a few hours and was handled without radioisotope. Further studies should be taken to detect telomerase activity in quantitation.

  2. Classification of Breast Cancer Subtypes by combining Gene Expression and DNA Methylation Data

    DEFF Research Database (Denmark)

    List, Markus; Hauschild, Anne-Christin; Tan, Qihua;


    on the transcriptomic, but also on an epigenetic level. We compared so-called random forest derived classification models based on gene expression and methylation data alone, to a model based on the combined features and to a model based on the gold standard PAM50. We obtained bootstrap errors of 10...

  3. Chromosome damage induced by DNA topoisomerase II inhibitors combined with g-radiation in vitro

    Directory of Open Access Journals (Sweden)

    Maria Cristina P. Araújo


    Full Text Available Combined radiation and antineoplastic drug treatment have important applications in cancer therapy. In the present work, an evaluation was made of two known topoisomerase II inhibitors, doxorubicin (DXR and mitoxantrone (MXN, with g-radiation. The effects of DXR or MXN on g-radiation-induced chromosome aberrations in Chinese hamster ovary (CHO cells were analyzed. Two concentrations of each drug, 0.5 and 1.0 µg/ml DXR, and 0.02 and 0.04 µg/ml MXN, were applied in combination with two doses of g-radiation (20 and 40 cGy. A significant potentiating effect on chromosomal aberrations was observed in CHO cells exposed to 1.0 µg/ml DXR plus 40 cGy. In the other tests, the combination of g-radiation with DXR or MXN gave approximately additive effects. Reduced mitotic indices reflected higher toxicity of the drugs when combined with radiation.A associação de radiação ionizante com drogas antineoplásicas tem importante aplicação na terapia do câncer. No presente trabalho, foram avaliados os efeitos de dois inibidores de topoisomerase II, doxorubicina (DXR e mitoxantrona (MXN, sobre as aberrações cromossômicas induzidas pelas radiações-g em células do ovário de hamster chinês (CHO. Foram usadas as concentrações 0,5 e 1,0 mg/ml de DXR e 0,02 e 0,04 mg/ml de MXN, combinadas com duas doses de radiações gama (20 e 40 cGy. Um significativo efeito potenciador das aberrações cromossômicas foi observado em células CHO tratadas com 1,0 mg/ml de DXR e expostas a 40 cGy de radiação. Nos outros testes, a combinação da radiação-g com a DXR ou MXN apresentou um efeito próximo ao aditivo. A redução dos índices mitóticos refletiu a alta citotoxicidade das drogas quando combinadas às radiações-g.

  4. Combination of small interfering RNAs mediates greater suppression on hepatitis B virus cccDNA in HepG2.2.15 cells

    Institute of Scientific and Technical Information of China (English)

    Xiao-Min Xin; Gui-Qiu U; Ying-Yu Jin; Min Zhuang; Di Li


    AIM: To observe the inhibition of hepatitis B virus (HBV) replication and expression in HepG2.2.15 cells by combination of small interfering RNAs (siRNAs).METHODS: Recombinant plasmid psil-HBV was constructed and transfected into HepG2.2.15 cells.At 48 h,72 h and 96 h after transfection,culture media were collected and cells were harvested for HBV replication assay.HBsAg and HBeAg in the cell culture medium were detected by enzyme-linked immunoadsorbent assay (ELISA).Intracellular viral DNA and covalently closed circular DNA (cccDNA)were quantified by real-time polymerase chain reaction (PCR).HBV viral mRNA was reverse transcribed and quantified by reverse-transcript PCR (RT-PCR).RESULTS: siRNAs showed marked anti-HBV effects.siRNAs could specifically inhibit the expression of HBsAg and the replication of HBV DNA in a dosedependent manner.Furthermore,combination of siRNAs,compared with individual use of each siRNA,exerted a stronger inhibition on antigen expression and viral replication.More importantly,combination of siRNAs significantly suppressed HBV cccDNA amplification.CONCLUSION: Combination of siRNAs mediates a stronger inhibition on viral replication and antigen expression in HepG2.2.15 cells,especially on cccDNA amplification.

  5. Combinations of various CpG motifs cloned into plasmid backbone modulate and enhance protective immunity of viral replicon DNA anthrax vaccines. (United States)

    Yu, Yun-Zhou; Ma, Yao; Xu, Wen-Hui; Wang, Shuang; Sun, Zhi-Wei


    DNA vaccines are generally weak stimulators of the immune system. Fortunately, their efficacy can be improved using a viral replicon vector or by the addition of immunostimulatory CpG motifs, although the design of these engineered DNA vectors requires optimization. Our results clearly suggest that multiple copies of three types of CpG motifs or combinations of various types of CpG motifs cloned into a viral replicon vector backbone with strong immunostimulatory activities on human PBMC are efficient adjuvants for these DNA vaccines to modulate and enhance protective immunity against anthrax, although modifications with these different CpG forms in vivo elicited inconsistent immune response profiles. Modification with more copies of CpG motifs elicited more potent adjuvant effects leading to the generation of enhanced immunity, which indicated a CpG motif dose-dependent enhancement of antigen-specific immune responses. Notably, the enhanced and/or synchronous adjuvant effects were observed in modification with combinations of two different types of CpG motifs, which provides not only a contribution to the knowledge base on the adjuvant activities of CpG motifs combinations but also implications for the rational design of optimal DNA vaccines with combinations of CpG motifs as "built-in" adjuvants. We describe an efficient strategy to design and optimize DNA vaccines by the addition of combined immunostimulatory CpG motifs in a viral replicon DNA plasmid to produce strong immune responses, which indicates that the CpG-modified viral replicon DNA plasmid may be desirable for use as vector of DNA vaccines.

  6. Combined TLR7/8 and TLR9 ligands potentiate the activity of a Schistosoma japonicum DNA vaccine.

    Directory of Open Access Journals (Sweden)

    Xuefeng Wang

    Full Text Available BACKGROUND: Toll-like receptor (TLR ligands have been explored as vaccine adjuvants for tumor and virus immunotherapy, but few TLR ligands affecting schistosoma vaccines have been characterized. Previously, we developed a partially protective DNA vaccine encoding the 26-kDa glutathione S-transferase of Schistosoma japonicum (pVAX1-Sj26GST. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we evaluated a TLR7/8 ligand (R848 and a TLR9 ligand (CpG oligodeoxynucleotides, or CpG as adjuvants for pVAX1-Sj26GST and assessed their effects on the immune system and protection against S. japonicum. We show that combining CpG and R848 with pVAX1-Sj26GST immunization significantly increases splenocyte proliferation and IgG and IgG2a levels, decreases CD4(+CD25(+Foxp3(+ regulatory T cells (Treg frequency in vivo, and enhances protection against S. japonicum. CpG and R848 inhibited Treg-mediated immunosuppression, upregulated the production of interferon (IFN-γ, tumor necrosis factor (TNF-α, interleukin (IL-4, IL-10, IL-2, and IL-6, and decreased Foxp3 expression in vitro, which may contribute to prevent Treg suppression and conversion during vaccination and allow expansion of antigen-specific T cells against pathogens. CONCLUSIONS: Our data shows that selective TLR ligands can increase the protective efficacy of DNA vaccines against schistosomiasis, potentially through combined antagonism of Treg-mediated immunosuppression and conversion.

  7. DNA methylation combinations in adjacent normal colon tissue predict cancer recurrence: evidence from a clinical cohort study.

    Directory of Open Access Journals (Sweden)

    Jen Chun Kuan

    Full Text Available Accumulating evidence has suggested the requirement for further stratification of patients in the same tumor stage according to molecular factors. We evaluate the combination of cancer stage and DNA methylation status as an indicator of the risk of recurrence and mortality among patients with colorectal cancer (CRC. A cohort study of 215 patients with CRC (mean age 64.32 years; 50.5% of men from Tri-Service General Hospital in Taiwan examined the association between cancer stage and risk of CRC recurrence and mortality. A Cox proportional hazard model was used to analyze patient methylation status and clinical information at study entry, and their associations with CRC recurrence and mortality during follow-up. The advanced stage patients with p16, hMLH1, and MGMT methylation were associated with higher risk of CRC recurrence compared with the local stage patients with unmethylation status in tumor tissues, with adjusted hazard ratios (HRs (95% confidence interval [CI] of 9.64 (2.92-31.81, 8.29 (3.40-20.22, and 11.83 (3.49-40.12, respectively. When analyzing normal tissues, we observed similar risk of CRC recurrence with adjusted HRs (95% CI of 10.85 (4.06-28.96, 9.04 (3.79-21.54, and 12.61 (4.90-32.44, respectively. For combined analyses, the risk of recurrence in the patients in advanced stage with DNA methylation in both normal and tumor tissues, compared with local stage with unmethylation, was increased with adjusted HR (95% CI of 9.37 (3.36-26.09. In the advanced stage patients, methylation status and tissue subtype were associated with increased risk of 5-year cumulative CRC recurrence (p < 0.001. This study demonstrates that clustering DNA methylation status according to cancer stage and tissue subtype is critical for the assessment of risk of recurrence in CRC patients and also indicated an underlying mechanism.

  8. Anti-dsDNA antibodies in systemic lupus erythematosus: A combination of two quantitative methods and the ANA pattern is the most efficient strategy of detection. (United States)

    Almeida González, Delia; Roces Varela, Alfredo; Marcelino Rodríguez, Itahisa; González Vera, Alexander; Delgado Sánchez, Mónica; Aznar Esquivel, Antonio; Casañas Rodríguez, Carlos; Cabrera de León, Antonio


    Several methods have been used to measure anti-double-stranded DNA auto-antibody (anti-dsDNA). Our aim was to determine the most efficient strategy to test anti-dsDNA in systemic lupus erythematosus (SLE). In this study, anti-dsDNA and anti-nuclear antibody (ANA) tests were requested for 644 patients. Anti-dsDNA was tested by RIA, ELISA and CLIA in all patients. The results indicated that 78 patients had a positive anti-dsDNA test according to at least one of the methods. After a 3-year follow-up period only 26 patients were diagnosed with SLE. We evaluated each method and combination of methods. Specificity and positive predictive value (PPV) increased with the number of assay methods used (p=0.002 for trend), and PPV was 100% in patients whose results were positive by all three anti-dsDNA assay methods. The proportion of anti-dsDNA-positive patients who had SLE was highest (82%; p b 0.001) among those with a homogeneous pattern of ANA staining, followed by those with a speckled pattern. In ANA positive patients, when only RIA was considered, 59% of anti-dsDNA-positive patients had SLE, but when RIA and CLIA were both considered, all patients with positive results on both tests had SLE. The combination of RIA+CLIA in patients with homogeneous and speckled ANA staining showed a similar cost and higher sensitivity than RIA alone in ANA positive patients (p b 0.001). We conclude that the most efficient strategy was to combine simultaneously two quantitative and sensitive methods but only in patients with a homogeneous or speckled pattern of ANA staining. This approach maximized specificity and PPV, and reduced costs.

  9. Study the effects of metallic ions on the combination of DNA and histones with molecular combing technique

    Institute of Scientific and Technical Information of China (English)

    LIU Yuying; WANG Pengye; DOU Shuoxing; XIE Ping; WANG Weichi; YIN Huawei


    The effects of monovalent (Na+, K+) and divalent (Mg2+, Ca2+, Mn2+) ions on the interaction between DNA and histone are studied using the molecular combing technique. λ-DNA molecules and DNA-histone complexes incubated with metal cations (Na+, K+, Mg2+, Ca2+, Mn2+) are stretched on hydrophobic surfaces, and directly observed by fluorescence microscopy. The results indicate that when these cations are added into the DNA solution, the fluorescence intensities of the stained DNA are reduced differently. The monovalent cations (Na+, K+) inhibit binding of histone to DNA. The divalent cations (Mg2+, Ca2+, Mn2+) enhance significantly the binding of histone to DNA and the binding of the DNA-histone complex to the hydrophobic surface. Mn2+ also induces condensation and aggregation of the DNA- histone complex.

  10. Changes in the response of MCF-7 cells to ionizing radiation after the combination of ATM and DNA-PK inhibition. (United States)

    Ćmielová, Jana; Havelek, Radim; Vávrová, Jiřina; Řezáčová, Martina


    The aim of the present study is to evaluate the role of ATM (KU55933) and DNA-PK (NU7441) inhibitors in the repair of double-strand breaks and downstream signaling of DNA damage introduced by ionizing radiation. The irradiation of MCF-7 cells alone increased the proportion of cells in the G1 phase in comparison with mock-treated cells. After ATM inhibitor pretreatment, the cells were more accumulated in the G2 phase, whereas DNA-PK inhibitor application increased the percentage of cells in the G1 phase. ATM and DNA-PK inhibitor application alone increased the sensitivity of MCF-7 cells to ionizing radiation; however, combining both inhibitors together resulted in a further enhancement of cell death. Unexpectedly, combining both inhibitors decreased the percentage of senescent cells and increased G2 cell cycle arrest 3 days after treatment. After irradiation, the p21 protein was increased and Chk1 and Chk2 were activated. These proteins were not increased in cells pretreated with the ATM inhibitor prior to ionizing radiation exposure, albeit DNA-PK inhibitor application did not affect the amount of proteins detected. Formation of γH2AX was found to be ATM and DNA-PK dependent, application of the ATM inhibitor suppressed incidence of γH2AX, whereas DNA-PK caused persistence of γH2AX. Our results suggest that the further investigation of the ATM inhibitor in combination with the DNA-PK inhibitor as sensitizers preventing cell senescence and promoting cell death in breast carcinoma MCF-7 cells is warranted.

  11. Combining morphology, DNA sequences, and morphometrics: revising closely related species in the orb-weaving spider genus Araniella (Araneae, Araneidae). (United States)

    Spasojevic, Tamara; Kropf, Christian; Nentwig, Wolfgang; Lasut, Liana


    The integration of independent data sets could solve problems in both traditional and DNA-based taxonomy. The aim of this study is to investigate the power of CO1 sequences and of morphometrics to distinguish closely related species in the spider genus Araniella. We put special emphasis on the species pair A. cucurbitina (Clerck, 1757) and A. opisthographa (Kulczyński, 1905) since the females are morphologically difficult to distinguish and often misidentified. A total of 216 sequences of eight Araniella species from seven European countries, North America and Asia were included in the molecular analysis. The results from both maximum likelihood and Bayesian phylogenetic inference indicate successful separation of six out of eight Araniella species, including A. cucurbitina and A. opisthographa. For the same six species, we detect no overlap of intra- and interspecific genetic divergence, leading to successful species identification with a threshold approach. In addition, morphometric analysis of the epigyna of A. cucurbitina and A. opisthographa supports species separation by two best explanatory ratios: receptaculum length and distance between receptaculum and copulatory duct. Although a small overlap in the ratios exists, the species identification rate increases when combining morphometric and molecular data, which demonstrates the efficiency of integrative approaches for distinguishing closely related species. However, none of the molecular approaches was able to separate closely related A. alpica (L. Koch, 1869) and A. inconspicua (Simon, 1874) due to shared CO1 haplotypes. Considering the clear morphological separation of the males and different habitat preferences, incomplete lineage sorting or introgressive hybridization could have led to identical CO1 sequences. Therefore, DNA-barcoding must be thoroughly tested even within small homogenous genera of spiders.

  12. Study the effects of divalent metallic ions on the combination of DNA and histones with fluorescence anisotropy assays

    Institute of Scientific and Technical Information of China (English)

    LIU YuYing; WANG PengYe; DOU ShuoXing; XIE Ping; XI XuGuang


    The effects of divalent ions (Mn2+, Mg2+, Ca2+) on the interaction between DNA and histone are studied using a fluorescence anisotropy assay. Fluorescence anisotropies of DNA and DNA-histone in the presence of divalent ions (Mn2+, Mg2+, Ca2+) are measured. The results indicate that histone reduces the fluorescence anisotropy of lambda DNA while the divalent ions (Mn2+, Mg2+, Ca2+) significantly enhance the fluorescence anisotropy. Compared to the case of DNA incubated with histone alone, there are more histones binding to DNA when divalent ion, histone and DNA are incubated together. We also find that Mn2+ makes the DNA-histone complexes more condensed than the other ions do.

  13. Mechanisms of immunotherapeutic intervention by anti-CD40L (CD154) antibody in an animal model of multiple sclerosis

    NARCIS (Netherlands)

    Howard, L.M.; Miga, A.J.; Vanderlugt, C.L.; Dal Canto, M.C.; Laman, J.D.; Noelle, R.J.; Miller, S.D.


    Relapsing experimental autoimmune encephalomyelitis (R-EAE) in the SJL mouse is a Th1-mediated autoimmune demyelinating disease model for human multiple sclerosis and is characterized by infiltration of the central nervous system (CNS) by Th1 cells and macrophages. Disease relapses are mediated by T

  14. Gene expression profiling of osteoclast differentiation by combined suppression subtractive hybridization (SSH) and cDNA microarray analysis. (United States)

    Rho, Jaerang; Altmann, Curtis R; Socci, Nicholas D; Merkov, Lubomir; Kim, Nacksung; So, Hongseob; Lee, Okbok; Takami, Masamichi; Brivanlou, Ali H; Choi, Yongwon


    Bone homeostasis is maintained by the balanced action of bone-forming osteoblasts and bone-resorbing osteoclasts. Multinucleated, mature osteoclasts develop from hematopoietic stem cells via the monocyte-macrophage lineage, which also give rise to macrophages and dendritic cells. Despite their distinct physiologic roles in bone and the immune system, these cell types share many molecular and biochemical features. To provide insights into how osteoclasts differentiate and function to control bone metabolism, we employed a systematic approach to profile patterns of osteoclast-specific gene expression by combining suppression subtractive hybridization (SSH) and cDNA microarray analysis. Here we examined how gene expression profiles of mature osteoclast differ from macrophage or dendritic cells, how gene expression profiles change during osteoclast differentiation, and how Mitf, a transcription factor critical for osteoclast maturation, affects the gene expression profile. This approach revealed a set of genes coordinately regulated for osteoclast function, some of which have previously been implicated in several bone diseases in humans.

  15. Gold Nanorods, DNA Origami, and Porous Silicon Nanoparticle-functionalized Biocompatible Double Emulsion for Versatile Targeted Therapeutics and Antibody Combination Therapy. (United States)

    Kong, Feng; Zhang, Hongbo; Qu, Xiangmeng; Zhang, Xu; Chen, Dong; Ding, Ruihua; Mäkilä, Ermei; Salonen, Jarno; Santos, Hélder A; Hai, Mingtan


    Gold nanorods, DNA origami, and porous silicon nanoparticle-functionalized biocompatible double emulsion are developed for versatile molecular targeted therapeutics and antibody combination therapy. This advanced photothermal responsive all-in-one biocompatible platform can be easily formed with great therapeutics loading capacity for different cancer treatments with synergism and multidrug resistance inhibition, which has great potential in advancing biomedical applications.

  16. On-line study of flavonoids of Trollius chinensis Bunge binding to DNA with ethidium bromide using a novel combination of chromatographic, mass spectrometric and fluorescence techniques. (United States)

    Song, Zhiling; Wang, Hong; Ren, Biao; Zhang, Baobao; Hashi, Yuki; Chen, Shizhong


    The study of the interaction between drugs and DNA is an important way to understand the role of drug molecules. A novel online analytical method for this purpose combining high-performance liquid chromatography-diode array detector-electrospray ionization-ion-trap time-of-flight mass spectrometry (HPLC-DAD-ESI-IT-TOF-MS(n)) and DNA-ethidium bromide detection with a fluorescence detector (DNA-EB-FLD) was firstly developed, which could rapidly identify the chemical constituents and obtain the profile related to DNA binding activity. This method has been applied for a precise or probable identification of the chemical constituents by ultraviolet (UV) absorption and MS(n) data analysis, while the DNA binding profile has been characterized by directly measuring the fluorescence intensity of compound-DNA-EB. Using this method, Trollius chinensis Bunge was studied and 18 constituents were identified by MS(n) data; six of them (4'-methoxy-2″-O-(2‴-methylbutyryl)vitexin,2″-O-(3‴-methoxycaffeoyl)vitexin) and 4'-methoxy-2″-O-(2‴-methylbutyryl)orientin,acacetin-7-O-rutinoside,quercetin-3-O-xylosylglucoside,quercetin-3-O-arabinosylglucoside) were identified for the first time in T. chinensis Bunge, and 16 constituents accounted for its activity of binding to DNA. The established (HPLC-DAD-ESI-IT-TOF-MS(n) DNA-EB-FLD) system has proved to offer a useful strategy for correlating the chemical profile with the binding to DNA activities of the components without their isolation and purification, and may be used for multicomponent analysis of active substances in other herbs.

  17. High-density DNA functionalization by a combination of Cu-catalyzed and cu-free click chemistry. (United States)

    Gutsmiedl, Katrin; Fazio, Danila; Carell, Thomas


    We report the regioselective Cu-free click modification of styrene functionalized DNA with nitrile oxides. A series of modified oligodeoxynucleotides (nine base pairs) was prepared with increasing styrene density. 1,3-Dipolar cycloaddition with nitrile oxides allows the high density functionalization of the styrene modified DNA directly on the DNA solid support and in solution. This click reaction proceeds smoothly even directly in the DNA synthesizer and gives exclusively 3,5-disubstituted isoxazolines. Additionally, PCR products (300 and 900 base pairs) were synthesized with a styrene triphosphate and KOD XL polymerase. The click reaction on the highly modified PCR fragments allows functionalization of hundreds of styrene units on these large DNA fragments simultaneously. Even sequential Cu-free and Cu-catalyzed click reaction of PCR amplicons containing styrene and alkyne carrying nucleobases was achieved. This new approach towards high-density functionalization of DNA is simple, modular, and efficient.

  18. DNA Damage and Inhibition of Akt Pathway in MCF-7 Cells and Ehrlich Tumor in Mice Treated with 1,4-Naphthoquinones in Combination with Ascorbate

    Directory of Open Access Journals (Sweden)

    Fabiana Ourique


    Full Text Available The aim of this study was to enhance the understanding of the antitumor mechanism of 1,4-naphthoquinones and ascorbate. Juglone, phenylaminonaphthoquinone-7, and 9 (Q7/Q9 were evaluated for effects on CT-DNA and DNA of cancer cells. Evaluations in MCF-7 cells are DNA damage, ROS levels, viability, and proliferation. Proteins from MCF-7 lysates were immunoblotted for verifying PARP integrity, γH2AX, and pAkt. Antitumor activity was measured in Ehrlich ascites carcinoma-bearing mice. The same markers of molecular toxicity were assessed in vivo. The naphthoquinones intercalate into CT-DNA and caused oxidative cleavage, which is increased in the presence of ascorbate. Treatments caused DNA damage and reduced viability and proliferation of MCF-7 cells. Effects were potentiated by ascorbate. No PARP cleavage was observed. Naphthoquinones, combined with ascorbate, caused phosphorylation of H2AX and inhibited pAkt. ROS were enhanced in MCF-7 cells, particularly by the juglone and Q7 plus ascorbate. Ehrlich carcinoma was inhibited by juglone, Q7, or Q9, but the potentiating effect of ascorbate was reproduced in vivo only in the cases of juglone and Q7, which caused up to 60% inhibition of tumor and the largest extension of survival. Juglone and Q7 plus ascorbate caused enhanced ROS and DNA damage and inhibited pAkt also in Ehrlich carcinoma cells.

  19. DNA damage and inhibition of akt pathway in mcf-7 cells and ehrlich tumor in mice treated with 1,4-naphthoquinones in combination with ascorbate. (United States)

    Ourique, Fabiana; Kviecinski, Maicon R; Felipe, Karina B; Correia, João Francisco Gomes; Farias, Mirelle S; Castro, Luiza S E P W; Grinevicius, Valdelúcia M A S; Valderrama, Jaime; Rios, David; Benites, Julio; Calderon, Pedro Buc; Pedrosa, Rozangela Curi


    The aim of this study was to enhance the understanding of the antitumor mechanism of 1,4-naphthoquinones and ascorbate. Juglone, phenylaminonaphthoquinone-7, and 9 (Q7/Q9) were evaluated for effects on CT-DNA and DNA of cancer cells. Evaluations in MCF-7 cells are DNA damage, ROS levels, viability, and proliferation. Proteins from MCF-7 lysates were immunoblotted for verifying PARP integrity, γH2AX, and pAkt. Antitumor activity was measured in Ehrlich ascites carcinoma-bearing mice. The same markers of molecular toxicity were assessed in vivo. The naphthoquinones intercalate into CT-DNA and caused oxidative cleavage, which is increased in the presence of ascorbate. Treatments caused DNA damage and reduced viability and proliferation of MCF-7 cells. Effects were potentiated by ascorbate. No PARP cleavage was observed. Naphthoquinones, combined with ascorbate, caused phosphorylation of H2AX and inhibited pAkt. ROS were enhanced in MCF-7 cells, particularly by the juglone and Q7 plus ascorbate. Ehrlich carcinoma was inhibited by juglone, Q7, or Q9, but the potentiating effect of ascorbate was reproduced in vivo only in the cases of juglone and Q7, which caused up to 60% inhibition of tumor and the largest extension of survival. Juglone and Q7 plus ascorbate caused enhanced ROS and DNA damage and inhibited pAkt also in Ehrlich carcinoma cells.

  20. Combined DNA and lipid analyses of sediments reveal changes in Holocene phytoplankton populations in an Antarctic lake

    NARCIS (Netherlands)

    Sinninghe Damsté, J.S.; Coolen, M.J.L.; Muyzer, G.; Rijpstra, W.I.C.; Schouten, S.; Volkman, J.K.


    Preserved ribosomal DNA of planktonic phototrophic algae was recovered from Holocene anoxic sediments of Ace Lake (Antarctica), and the ancient community members were identified based on comparative sequence analysis. The similar concentration profiles of DNA of haptophytes and their traditional lip

  1. Rapid, highly sensitive and highly specific gene detection by combining enzymatic amplification and DNA chip detection simultaneously

    Directory of Open Access Journals (Sweden)

    Koji Hashimoto


    Full Text Available We have developed a novel gene detection method based on the loop-mediated isothermal amplification (LAMP reaction and the DNA dissociation reaction on the same DNA chip surface to achieve a lower detection limit, broader dynamic range and faster detection time than are attainable with a conventional DNA chip. Both FAM- and thiol-labeled DNA probe bound to the complementary sequence accompanying Dabcyl was immobilized on the gold surface via Au/thiol bond. The LAMP reaction was carried out on the DNA probe fixed gold surface. At first, Dabcyl molecules quenched the FAM fluorescence. According to the LAMP reaction, the complementary sequence with Dabcyl was competitively reacted with the amplified targeted sequence. As a result, the FAM fluorescence increased owing to dissociation of the complementary sequence from the DNA probe. The simultaneous reaction of LAMP and DNA chip detection was achieved, and 103 copies of the targeted gene were detected within an hour by measuring fluorescence intensity of the DNA probe.

  2. Oxidized dNTPs and the OGG1 and MUTYH DNA glycosylases combine to induce CAG/CTG repeat instability (United States)

    Cilli, Piera; Ventura, Ilenia; Minoprio, Anna; Meccia, Ettore; Martire, Alberto; Wilson, Samuel H.; Bignami, Margherita; Mazzei, Filomena


    DNA trinucleotide repeat (TNR) expansion underlies several neurodegenerative disorders including Huntington's disease (HD). Accumulation of oxidized DNA bases and their inefficient processing by base excision repair (BER) are among the factors suggested to contribute to TNR expansion. In this study, we have examined whether oxidation of the purine dNTPs in the dNTP pool provides a source of DNA damage that promotes TNR expansion. We demonstrate that during BER of 8-oxoguanine (8-oxodG) in TNR sequences, DNA polymerase β (POL β) can incorporate 8-oxodGMP with the formation of 8-oxodG:C and 8-oxodG:A mispairs. Their processing by the OGG1 and MUTYH DNA glycosylases generates closely spaced incisions on opposite DNA strands that are permissive for TNR expansion. Evidence in HD model R6/2 mice indicates that these DNA glycosylases are present in brain areas affected by neurodegeneration. Consistent with prevailing oxidative stress, the same brain areas contained increased DNA 8-oxodG levels and expression of the p53-inducible ribonucleotide reductase. Our in vitro and in vivo data support a model where an oxidized dNTPs pool together with aberrant BER processing contribute to TNR expansion in non-replicating cells. PMID:26980281

  3. Additives and Protein-DNA Combinations Modulate the Humoral Immune Response Elicited by a Hepatitis C Virus Core-encoding Plasmid in Mice

    Directory of Open Access Journals (Sweden)

    Alvarez-Lajonchere Liz


    Full Text Available Humoral and cellular immune responses are currently induced against hepatitis C virus (HCV core following vaccination with core-encoding plasmids. However, the anti-core antibody response is frequently weak or transient. In this paper, we evaluated the effect of different additives and DNA-protein combinations on the anti-core antibody response. BALB/c mice were intramuscularly injected with an expression plasmid (pIDKCo, encoding a C-terminal truncated variant of the HCV core protein, alone or combined with CaCl2, PEG 6000, Freund's adjuvant, sonicated calf thymus DNA and a recombinant core protein (Co.120. Mixture of pIDKCo with PEG 6000 and Freund's adjuvant accelerated the development of the anti-core Ab response. Combination with PEG 6000 also induced a bias to IgG2a subclass predominance among anti-core antibodies. The kinetics, IgG2a/IgG1 ratio and epitope specificity of the anti-core antibody response elicited by Co.120 alone or combined with pIDKCo was different regarding that induced by the pIDKCo alone. Our data indicate that the antibody response induced following DNA immunization can be modified by formulation strategies.

  4. Transient B-cell depletion with anti-CD20 in combination with proinsulin DNA vaccine or oral insulin: immunologic effects and efficacy in NOD mice.

    Directory of Open Access Journals (Sweden)

    Ghanashyam Sarikonda

    Full Text Available A recent type 1 diabetes (T1D clinical trial of rituximab (a B cell-depleting anti-CD20 antibody achieved some therapeutic benefit in preserving C-peptide for a period of approximately nine months in patients with recently diagnosed diabetes. Our previous data in the NOD mouse demonstrated that co-administration of antigen (insulin with anti-CD3 antibody (a T cell-directed immunomodulator offers better protection than either entity alone, indicating that novel combination therapies that include a T1D-related autoantigen are possible. To accelerate the identification and development of novel combination therapies that can be advanced into the clinic, we have evaluated the combination of a mouse anti-CD20 antibody with either oral insulin or a proinsulin-expressing DNA vaccine. Anti-CD20 alone, given once or on 4 consecutive days, produced transient B cell depletion but did not prevent or reverse T1D in the NOD mouse. Oral insulin alone (twice weekly for 6 weeks was also ineffective, while proinsulin DNA (weekly for up to 12 weeks showed a trend toward modest efficacy. Combination of anti-CD20 with oral insulin was ineffective in reversing diabetes in NOD mice whose glycemia was controlled with SC insulin pellets; these experiments were performed in three independent labs. Combination of anti-CD20 with proinsulin DNA was also ineffective in diabetes reversal, but did show modest efficacy in diabetes prevention (p = 0.04. In the prevention studies, anti-CD20 plus proinsulin resulted in modest increases in Tregs in pancreatic lymph nodes and elevated levels of proinsulin-specific CD4+ T-cells that produced IL-4. Thus, combination therapy with anti-CD20 and either oral insulin or proinsulin does not protect hyperglycemic NOD mice, but the combination with proinsulin offers limited efficacy in T1D prevention, potentially by augmentation of proinsulin-specific IL-4 production.

  5. A combination DNA vaccine encoding nucleoside hydrolase 36 and glycoproteine 63 protects female but not male hamsters against Leishmania mexicana

    Directory of Open Access Journals (Sweden)

    Chalé-balboa W.G.


    Full Text Available Leishmaniasis is a group of diseases caused by protozoan parasites of the Leishmania genus. Previous studies have shown that a DNA vaccine encoding Leishmania donovani antigen nucleoside hydrolase 36 and L. mexicana glycoprotein 63 is protective in mice. We investigated here the efficacy of this DNA vaccine to induce protection in golden hamsters. Male hamsters were more susceptible to infection by Leishmania mexicana than females. Following immunization with two doses of the DNA vaccine, only females resulted protected while males developed normal lesions.

  6. One simple DNA extraction device and its combination with modified visual loop-mediated isothermal amplification for rapid on-field detection of genetically modified organisms. (United States)

    Zhang, Miao; Liu, Yinan; Chen, Lili; Quan, Sheng; Jiang, Shimeng; Zhang, Dabing; Yang, Litao


    Quickness, simplicity, and effectiveness are the three major criteria for establishing a good molecular diagnosis method in many fields. Herein we report a novel detection system for genetically modified organisms (GMOs), which can be utilized to perform both on-field quick screening and routine laboratory diagnosis. In this system, a newly designed inexpensive DNA extraction device was used in combination with a modified visual loop-mediated isothermal amplification (vLAMP) assay. The main parts of the DNA extraction device included a silica gel membrane filtration column and a modified syringe. The DNA extraction device could be easily operated without using other laboratory instruments, making it applicable to an on-field GMO test. High-quality genomic DNA (gDNA) suitable for polymerase chain reaction (PCR) and isothermal amplification could be quickly isolated from plant tissues using this device within 15 min. In the modified vLAMP assay, a microcrystalline wax encapsulated detection bead containing SYBR green fluorescent dye was introduced to avoid dye inhibition and cross-contaminations from post-LAMP operation. The system was successfully applied and validated in screening and identification of GM rice, soybean, and maize samples collected from both field testing and the Grain Inspection, Packers, and Stockyards Administration (GIPSA) proficiency test program, which demonstrated that it was well-adapted to both on-field testing and/or routine laboratory analysis of GMOs.

  7. Allelic frequency distributions of 21 non-combined DNA index system STR loci in a Russian ethnic minority group from Inner Mongolia, China*


    Wang, Hong-Dan; Shen, Chun-Mei; Liu, Wen-Juan; Zhang, Yu-Dang; Yang, Guang; Yan, Jiang-wei; Qin, Hai-Xia; Zhu, Bo-Feng


    We studied the allelic frequency distributions and statistical forensic parameters of 21 new short tandem repeat (STR) loci and the amelogenin locus, which are not included in the combined DNA index system (CODIS), in a Russian ethnic minority group from the Inner Mongolia Autonomous Region, China. A total of 114 bloodstain samples from unrelated individuals were extracted and co-amplified with four fluorescence-labeled primers in a multiplex polymerase chain reaction (PCR) system. Using capi...

  8. The synergistic effect of combined immunization with a DNA vaccine and chimeric yellow fever/dengue virus leads to strong protection against dengue.

    Directory of Open Access Journals (Sweden)

    Adriana S Azevedo

    Full Text Available The dengue envelope glycoprotein (E is the major component of virion surface and its ectodomain is composed of domains I, II and III. This protein is the main target for the development of a dengue vaccine with induction of neutralizing antibodies. In the present work, we tested two different vaccination strategies, with combined immunizations in a prime/booster regimen or simultaneous inoculation with a DNA vaccine (pE1D2 and a chimeric yellow fever/dengue 2 virus (YF17D-D2. The pE1D2 DNA vaccine encodes the ectodomain of the envelope DENV2 protein fused to t-PA signal peptide, while the YF17D-D2 was constructed by replacing the prM and E genes from the 17D yellow fever vaccine virus by those from DENV2. Balb/c mice were inoculated with these two vaccines by different prime/booster or simultaneous immunization protocols and most of them induced a synergistic effect on the elicited immune response, mainly in neutralizing antibody production. Furthermore, combined immunization remarkably increased protection against a lethal dose of DENV2, when compared to each vaccine administered alone. Results also revealed that immunization with the DNA vaccine, regardless of the combination with the chimeric virus, induced a robust cell immune response, with production of IFN-γ by CD8+ T lymphocytes.

  9. The synergistic effect of combined immunization with a DNA vaccine and chimeric yellow fever/dengue virus leads to strong protection against dengue. (United States)

    Azevedo, Adriana S; Gonçalves, Antônio J S; Archer, Marcia; Freire, Marcos S; Galler, Ricardo; Alves, Ada M B


    The dengue envelope glycoprotein (E) is the major component of virion surface and its ectodomain is composed of domains I, II and III. This protein is the main target for the development of a dengue vaccine with induction of neutralizing antibodies. In the present work, we tested two different vaccination strategies, with combined immunizations in a prime/booster regimen or simultaneous inoculation with a DNA vaccine (pE1D2) and a chimeric yellow fever/dengue 2 virus (YF17D-D2). The pE1D2 DNA vaccine encodes the ectodomain of the envelope DENV2 protein fused to t-PA signal peptide, while the YF17D-D2 was constructed by replacing the prM and E genes from the 17D yellow fever vaccine virus by those from DENV2. Balb/c mice were inoculated with these two vaccines by different prime/booster or simultaneous immunization protocols and most of them induced a synergistic effect on the elicited immune response, mainly in neutralizing antibody production. Furthermore, combined immunization remarkably increased protection against a lethal dose of DENV2, when compared to each vaccine administered alone. Results also revealed that immunization with the DNA vaccine, regardless of the combination with the chimeric virus, induced a robust cell immune response, with production of IFN-γ by CD8+ T lymphocytes.

  10. DNA Polymerases η and ζ Combine to Bypass O(2)-[4-(3-Pyridyl)-4-oxobutyl]thymine, a DNA Adduct Formed from Tobacco Carcinogens. (United States)

    Gowda, A S Prakasha; Spratt, Thomas E


    4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) and N'-nitrosonornicotine (NNN) are important human carcinogens in tobacco products. They are metabolized to produce a variety 4-(3-pyridyl)-4-oxobutyl (POB) DNA adducts including O(2)-[4-(3-pyridyl)-4-oxobut-1-yl]thymidine (O(2)-POB-dT), the most abundant POB adduct in NNK- and NNN-treated rodents. To evaluate the mutagenic properties of O(2)-POB-dT, we measured the rate of insertion of dNTPs opposite and extension past O(2)-POB-dT and O(2)-Me-dT by purified human DNA polymerases η, κ, ι, and yeast polymerase ζ in vitro. Under conditions of polymerase in excess, polymerase η was most effective at the insertion of dNTPs opposite O(2)-alkyl-dTs. The time courses were biphasic suggesting the formation of inactive DNA-polymerase complexes. The kpol parameter was reduced approximately 100-fold in the presence of the adduct for pol η, κ, and ι. Pol η was the most reactive polymerase for the adducts due to a higher burst amplitude. For all three polymerases, the nucleotide preference was dATP > dTTP ≫ dGTP and dCTP. Yeast pol ζ was most effective in bypassing the adducts; the kcat/Km values were reduced only 3-fold in the presence of the adducts. The identity of the nucleotide opposite the O(2)-alkyl-dT did not significantly affect the ability of pol ζ to bypass the adducts. The data support a model in which pol η inserts ATP or dTTP opposite O(2)-POB-dT, and then, pol ζ extends past the adduct.


    Institute of Scientific and Technical Information of China (English)

    ZHANG; Kai-tai


    [1]Tom S, Andrew PR. Human Molecular Genetics [M]. John Wiley & Sons, Inc. United States of America 1996; 335.[2]Zhao Yong-liang, Jin Cui-zhen, Wu De-chang et al. Neoplastic transformation and cytogenetic changes of rat tracheal epithelial cells induced by a-particles irradiation [J]. Chin Med Sci J 1997; 12:202.[3]Frohman MA. Rapid amplification of complementary DNA ends for generation of full-length complementary DNAs: thermal RACE [J]. Methods Enzymol 1993; 218:340.[4]Frederick A, Roger B. Current Protocols in Molecular Biology [M]. John Wiley & Sons, Inc. United States of America 1998; 2.1.1.[5]Roux KH. Optimization and troubleshooting in PCR [J]. PCR Methods Appl 1995; 4:5158.[6]Sambrook, J, Fritsch EF, Maniatis T. Molecular Cloning: A Laboratory Manual [M]. 2nd Ed. New York: Cold Spring Harbor Laboratory, Cold Spring Harbor, 1989; 54.[7]Zhang Y, Frohman MA. Using rapid amplification of cDNA ends (RACE) to obtain full-length cDNAs [J]. Methods Mol Biol 1997; 69:61.[8]Frohman MA. Rapid amplification of complementary DNA ends for generation of full-length complementary DNAs: thermal RACE [J]. Methods Enzymol 1993; 218:340.[9]Iqbal S, Robinson J, Deere D, et al. Efficiency of the polymerase chain reaction amplification of the uid gene for detection of Escherichia coli in contaminated water [J]. Lett Appl Microbiol 1997; 24:498.[10]Schunck B, Kraft W, Truyen U. A simple touch-down polymerase chain reaction for the detection of canine parvovirus and feline panleukopenia virus in feces [J]. J Virol Methods 1995; 55:427.

  12. 日本血吸虫DNA疫苗联合免疫的研究进展%Research Progress on combined immunization of DNA vaccine against Schistosoma japonicum

    Institute of Scientific and Technical Information of China (English)

    冯其梅; 张树菊; 汪世平


    疫苗作为预防和控制传染病的重要手段,已成功的控制了很多传染病的流行.因此,许多研究者希望研制一种安全有效的血吸虫病疫苗,以期达到控制血吸虫病流行的目的.近年来,鉴于单价疫苗有限的免疫效果,人们开始进行日本血吸虫DNA疫苗联合免疫的研究.本文对日本血吸虫DNA疫苗联合免疫的研究资料进行了归纳整理,发现日本血吸虫DNA疫苗联合免疫涉及鸡尾酒式DNA混合疫苗、双价和多价DNA联合疫苗以及佐剂研究等方面,比较减虫卒、减卵率等指标,联合免疫疫苗的效果明显优于单价DNA疫苗的效果,而且具有潜在的实际应用价值.%As an important mean of prevention and control of infectious diseases, vaccine has been successfully took control. Therefore, in order to control the prevalence of sehistosomiasis japonica, many scientists want to develop a safe and effective vaccine against Schistosoma japonicum. Recently, in view of the limited immune effect of monovalent vaccine, people have started to study combined immunization of DNA vaccine of Schistosoma japonicum. This paper review the development of combined immunization of DNA vaccine against Schistosoma japonicum , and found that combined DNA vaccines include cocktail hybrid DNA vaccines, bivalent and multivalent DNA vaccines, and DNA vaccines with adjuvant mainly. They induced higher worm reduction rate and liver egg reduction rate, and would be well worthy of to be study.

  13. Arsenic-Induced Antioxidant Depletion, Oxidative DNA Breakage, and Tissue Damages are Prevented by the Combined Action of Folate and Vitamin B12. (United States)

    Acharyya, Nirmallya; Deb, Bimal; Chattopadhyay, Sandip; Maiti, Smarajit


    Arsenic is a grade I human carcinogen. It acts by disrupting one-carbon (1C) metabolism and cellular methyl (-CH3) pool. The -CH3 group helps in arsenic disposition and detoxification of the biological systems. Vitamin B12 and folate, the key promoters of 1C metabolism were tested recently (daily 0.07 and 4.0 μg, respectively/100 g b.w. of rat for 28 days) to evaluate their combined efficacy in the protection from mutagenic DNA-breakage and tissue damages. The selected tissues like intestine (first-pass site), liver (major xenobiotic metabolizer) and lung (major arsenic accumulator) were collected from arsenic-ingested (0.6 ppm/same schedule) female rats. The hemo-toxicity and liver and kidney functions were monitored. Our earlier studies on arsenic-exposed humans can correlate carcinogenesis with DNA damage. Here, we demonstrate that the supplementation of physiological/therapeutic dose of vitamin B12 and folate protected the rodents significantly from arsenic-induced DNA damage (DNA fragmentation and comet assay) and hepatic and renal tissue degeneration (histo-architecture, HE staining). The level of arsenic-induced free-radical products (TBARS and conjugated diene) was significantly declined by the restored actions of several antioxidants viz. urate, thiol, catalase, xanthine oxidase, lactoperoxidase, and superoxide dismutase in the tissues of vitamin-supplemented group. The alkaline phosphatase, transaminases, urea and creatinine (hepatic and kidney toxicity marker), and lactate dehydrogenase (tissue degeneration marker) were significantly impaired in the arsenic-fed group. But a significant protection was evident in the vitamin-supplemented group. In conclusion, the combined action of folate and B12 results in the restitution in the 1C metabolic pathway and cellular methyl pool. The cumulative outcome from the enhanced arsenic methylation and antioxidative capacity was protective against arsenic induced mutagenic DNA breakages and tissue damages.

  14. Effect of alprostadil combined with conventional therapy on serum markers in patients with acute cerebral infarction

    Institute of Scientific and Technical Information of China (English)

    Li-Lan Chen; Guo-Qiang Chen; Tao Yang; Mu-Qing Long


    Objective:To study the effect of alprostadil combined with conventional therapy on serum markers in patients with acute cerebral infarction.Methods:Patients with acute cerebral infarction treated in our hospital from May 2012 to August 2014 were enrolled and randomly divided into two groups. Observation group received alprostadil combined with conventional therapy and control group received conventional treatment. Then serum markers of both groups were compared.Results:(1) contents of serum nerve function related molecules: serum NSE and S100βcontents of observation group showed a decreasing trend, and BDNF and NGF contents showed an increasing trend; (2) contents of atherosclerosis related enzymes: serum GGT, iNOS and MPO contents of observation group showed a decreasing trend, and PON1 and PON2 contents showed an increasing trend; (3) platelet activation related molecules: serum PPARγ, CD62p, YKL-40, sCD40L and Fibulin-5 contents of observation group all showed a decreasing trend.Conclusions:Alprostadil combined with conventional treatment is helpful to alleviate neuronal damage and inhibit the processes of atherosclerosis and platelet activation;it’s an ideal method for treating acute cerebral infarction.

  15. Combined treatment with vitamin B12b and ascorbic acid causes in vitro DNA degradation in tumor cells. (United States)

    Medvedev, A I; Akatov, V S; Kreshchenko, N D; Solov'eva, M E; Leshchenko, V V; Lezhnev, E I; Yakubovskaya, R I


    Incubation of Ehrlich ascites carcinoma and HEp-2 human epidermoid laryngeal carcinoma cells with hydroxycobalamin (vitamin B12b) and ascorbic acid induced generation and accumulation of double-stranded DNA fragments (23,000 b.p. and longer) in cells. The same vitamins alone in the same concentrations produced no such effects. DNA degradation in HEp-2 cells caused by long-term (4 h) incubation with 5-25 microM hydroxycobalamin and ascorbic acid (1:10-1:40 molar ratio) at 37 degrees C was comparable with that induced by gamma-irradiation in a dose of 150 Gy at 4 degrees C.

  16. Effect of a combination DNA vaccine for the prevention and therapy of Trypanosoma cruzi infection in mice: role of CD4+ and CD8+ T cells. (United States)

    Limon-Flores, Alberto Yairh; Cervera-Cetina, Rodrigo; Tzec-Arjona, Juan L; Ek-Macias, Lorena; Sánchez-Burgos, Gilma; Ramirez-Sierra, Maria J; Cruz-Chan, J Vladimir; VanWynsberghe, Nicole R; Dumonteil, Eric


    Chagas disease is a major public health problem, with about 10 million infected people, and DNA vaccines are a promising alternative for the control of Trypanosoma cruzi, the causing agent of the disease. We tested here a new DNA vaccine encoding a combination of two leading parasite antigens, TSA-1 and Tc24, for the prevention and therapy of T. cruzi infection. Immunized Balb/c mice challenged by T. cruzi presented a significantly lower parasitemia and inflammatory cell density in the heart compared to control mice. Similarly, the therapeutic administration of the DNA vaccine was able to significantly reduce the parasitemia and inflammatory reaction in acutely infected Balb/c and C57BL/6 mice, and reduced cardiac tissue inflammation in chronically infected ICR mice. Therapeutic vaccination induced a marked increase in parasite-specific IFNγ producing CD4(+) and CD8(+) T cells in the spleen as well as an increase in CD4(+) and CD8(+) T cells in the infected cardiac tissue. In addition, some effect of the DNA vaccine could still be observed in CD4-knockout C57BL/6 mice, which presented a lower parasitemia and inflammatory cell density, but not in CD8-deficient mice, in which the vaccine had no effect. These results indicate that the activation of CD8(+) T cells plays a major role in the control of the infection by the therapeutic DNA vaccine, and to a somewhat lesser extent CD4(+) T cells. This observation opens interesting perspectives for the potentiation of this DNA vaccine candidate by including additional CD8(+) T cell antigens/epitopes in future vaccine formulations.

  17. The combined effects of BDE47 and BaP on oxidatively generated DNA damage in L02 cells and the possible molecular mechanism. (United States)

    An, Jing; Yin, Lingling; Shang, Yu; Zhong, Yufang; Zhang, Xinyu; Wu, Minghong; Yu, Zhiqiang; Sheng, Guoying; Fu, Jiamo; Huang, Yuecheng


    Polybrominated diphenyl ethers (PBDEs) and polycyclic aromatic hydrocarbons (PAHs) coexist widely in the environment and have generated adverse effects on the environment and human health. The purpose of this study was to investigate the combined toxic effects of these chemicals and the related mechanism. L02 cells were exposed to BDE47 (5, 10μmol/L) or/and BaP (50μmol/L) in different administration order. The cell growth and survival, DNA strand breaks, oxidative stress index (ROS, SOD, GSH, and MDA), LDH release and the expression level of CYP1 family members were measured. The result showed that BDE47 or/and BaP had no effect on the cell growth and survival under the present conditions. However, compared with the groups treated with BDE47 or BaP alone, the combined-treated groups induced significantly elevated DNA strand breaks, ROS production, and MDA level. Especially, pretreatment with BDE47 followed by BaP led to the strongest effects. Addition of the antioxidant N-acetyl-l-cysteine (NAC) markedly reduced the ROS level and partly suppressed the DNA strand breaks induced by BDE47 or/and BaP. Meanwhile, the combined treatment groups also markedly increased the SOD activity, GSH content, and LDH release level compared with the control group. The real-time PCR results showed that BaP could significantly induce the expression of CYP1A1 and CYP1B1, however, the pre-treatment with BDE47 appeared to attenuate the BaP-induced CYP1 expression. All of above findings indicated that BDE47 and BaP had a synergistic effect on oxidatively generated DNA damage in L02 cells via regulation on the oxidative stress response and the expression of CYP1 metabolism enzymes.

  18. DNA origami nanopores for controlling DNA translocation. (United States)

    Hernández-Ainsa, Silvia; Bell, Nicholas A W; Thacker, Vivek V; Göpfrich, Kerstin; Misiunas, Karolis; Fuentes-Perez, Maria Eugenia; Moreno-Herrero, Fernando; Keyser, Ulrich F


    We combine DNA origami structures with glass nanocapillaries to reversibly form hybrid DNA origami nanopores. Trapping of the DNA origami onto the nanocapillary is proven by imaging fluorescently labeled DNA origami structures and simultaneous ionic current measurements of the trapping events. We then show two applications highlighting the versatility of these DNA origami nanopores. First, by tuning the pore size we can control the folding of dsDNA molecules ("physical control"). Second, we show that the specific introduction of binding sites in the DNA origami nanopore allows selective detection of ssDNA as a function of the DNA sequence ("chemical control").

  19. Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation

    NARCIS (Netherlands)

    Colomé Tatché, Maria; Cortijo, Sandra; Wardenaar, Rene; Monteiro Morgado, Lionel; Lahouze, Benoit; Sarazin, Alexis; Etcheverry, Mathilde; Martin, Antoine; Feng, Suhua; Duvernois-Berthet, Evelyne; Labadie, Karine; Wincker, Patrick; Jacobsen, Steven E.; Jansen, Ritsert C.; Colot, Vincent; Johannes, Frank


    The rate of meiotic crossing over (CO) varies considerably along chromosomes, leading to marked distortions between physical and genetic distances. The causes underlying this variation are being unraveled, and DNA sequence and chromatin states have emerged as key factors. However, the extent to whic

  20. Development of a 24-locus multiplex system to incorporate the core loci in the Combined DNA Index System (CODIS) and the European Standard Set (ESS). (United States)

    Guo, Fei; Shen, Hongying; Tian, Huaizhou; Jin, Ping; Jiang, Xianhua


    The 24-locus multiplex system allows co-amplification and fluorescent detection of 24 loci (23 STR loci and Amelogenin), including STR loci in the Combined DNA Index System (CODIS) and the ESS (European Standard Set) as well as five additional loci (D2S1338, D6S1043, D19S433, Penta D and Penta E) commonly used in commercial kits. It facilitates data sharing and minimizes adventitious matches within national or between international DNA databases. Additionally, the system can amplify directly from blood and buccal samples spotted on filter paper and swabs and reduce the cycling time to less than one hour and a half. Primers, internal size standard, allelic ladders and matrix standard set were designed and created in-house with a design strategy to work in this multiplex. Developmental validation experiments followed the Scientific Working Group on DNA Analysis Methods (SWGDAM) and the Chinese National Standard (GA/T815-2009) guidelines. The system was evaluated by species specificity, sensitivity, stability, precision and accuracy, case-type samples, population, mixture and PCR-based studies. The results demonstrate that the 24-locus multiplex system is a robust and reliable identification assay as required for forensic DNA typing and databasing.

  1. Cooperative binding of PhoB(DBD) to its cognate DNA sequence-a combined application of single-molecule and ensemble methods. (United States)

    Ritzefeld, Markus; Walhorn, Volker; Kleineberg, Christin; Bieker, Adeline; Kock, Klaus; Herrmann, Christian; Anselmetti, Dario; Sewald, Norbert


    A combined approach based on isothermal titration calorimetry (ITC), fluorescence resonance energy transfer (FRET) experiments, circular dichroism spectroscopy (CD), atomic force microscopy (AFM) dynamic force spectroscopy (DFS), and surface plasmon resonance (SPR) was applied to elucidate the mechanism of protein-DNA complex formation and the impact of protein dimerization of the DNA-binding domain of PhoB (PhoB(DBD)). These insights can be translated to related members of the family of winged helix-turn-helix proteins. One central question was the assembly of the trimeric complex formed by two molecules of PhoB(DBD) and two cognate binding sites of a single oligonucleotide. In addition to the native protein WT-PhoB(DBD), semisynthetic covalently linked dimers with different linker lengths were studied. The ITC, SPR, FRET, and CD results indicate a positive cooperative binding mechanism and a decisive contribution of dimerization on the complex stability. Furthermore, an alanine scan was performed and binding of the corresponding point mutants was analyzed by both techniques to discriminate between different binding types involved in the protein-DNA interaction and to compare the information content of the two methods DFS and SPR. In light of the published crystal structure, four types of contribution to the recognition process of the pho box by the protein PhoB(DBD) could be differentiated and quantified. Consequently, it could be shown that investigating the interactions between DNA and proteins with complementary techniques is necessary to fully understand the corresponding recognition process.

  2. Membrane Destruction and DNA Binding of Staphylococcus aureus Cells Induced by Carvacrol and Its Combined Effect with a Pulsed Electric Field. (United States)

    Wang, Lang-Hong; Wang, Man-Sheng; Zeng, Xin-An; Zhang, Zhi-Hong; Gong, De-Ming; Huang, Yan-Bo


    Carvacrol (5-isopropyl-2-methylphenol, CAR) is an antibacterial ingredient that occurs naturally in the leaves of the plant Origanum vulgare. The antimicrobial mechanism of CAR against Staphylococcus aureus ATCC 43300 was investigated in the study. Analysis of the membrane fatty acids by gas chromatography-mass spectrometry (GC-MS) showed that exposure to CAR at low concentrations induced a marked increase in the level of unbranched fatty acids (from 34.90 ± 1.77% to 62.37 ± 4.26%). Moreover, CAR at higher levels severely damaged the integrity and morphologies of the S. aureus cell membrane. The DNA-binding properties of CAR were also investigated using fluorescence, circular dichroism, molecular modeling, and atomic-force microscopy. The results showed that CAR bound to DNA via the minor-groove mode, mildly perturbed the DNA secondary structure, and induced DNA molecules to be aggregated. Furthermore, a combination of CAR with a pulsed-electric field was found to exhibit strong synergistic effects on S. aureus.

  3. Visual recovery in a man with the rare combination of mtDNA 11778 LHON mutation and a MS-like disease after mitoxantrone therapy. (United States)

    Buhmann, C; Gbadamosi, J; Heesen, C


    We describe a young man with prognostic unfavourable homoplasmatic mitochondrial DNA(mt DNA) 11778 Leber's hereditary optic neuropathy (LHON) point mutation and confirmed multiple sclerosis (MS). This combination of LHON and MS-like disease is rare in both sexes, and in men has been described in only a few case reports. In a 4-year follow-up during immunosuppressive therapy with mitoxantrone, we found a remarkable time delayed visual recovery 12 months after acute onset of rapid sequential bilateral subtotal visual loss followed by episodes of isolated acute demyelinative optic neuropathy. Visual recovery to such extent after this latency is uncommon in both mtDNA 11778 LHON mutation and optic neuritis (ON) in MS. Relapses in visual deterioration must be considered as extremely rare in LHON. This case might support the hypothesis of an immunological pathogenetic factor in combined LHON and MS, and possibly in LHON alone. We suggest a search for the LHON mutation in MS patients with predominant visual impairment, independent of patients' gender.

  4. Combination of 768-well microplate array diagonal gel electrophoresis with duplex PCR of X and Y chromosome markers for quality control of epidemiological DNA banks. (United States)

    Huang, Shuwen; Chen, Xiao-he; Day, Ian N M


    Large DNA banks for human epidemiological studies have become an increasingly important research tool. The power of genotype-phenotype studies is dependent both on the quality of phenotyping and of genotyping and of correct linking of phenotypes to genotypes. Samples must be tracked through numerous steps between subject or patient and post-genotypic data. Only one phenotype, sex, has a perfect and binary correlation with genotype. In mixed sex studies, it may be advantageous for purposes of quality control to keep sexes mixed during the steps from acquisition to DNA bank, in order to be able to check later for sample swaps. We have designed a duplex PCR combining an amplicon from MAOA marking the X chromosome and an amplicon from DDX3Y marking the Y chromosome. We combined this with a simple economical palmtop sized 768-well microplate compatible electrophoresis system developed in-house for examination of duplex PCR products. We applied this quality control test in the validation of two DNA banks.

  5. Enhanced anti-tumor effect of zoledronic acid combined with temozolomide against human malignant glioma cell expressing O6-methylguanine DNA methyltransferase.

    Directory of Open Access Journals (Sweden)

    Junya Fukai

    Full Text Available Temozolomide (TMZ, a DNA methylating agent, is widely used in the adjuvant treatment of malignant gliomas. O6-methylguanine-DNA methyltranferase (MGMT, a DNA repair enzyme, is frequently discussed as the main factor that limits the efficacy of TMZ. Zoledronic acid (ZOL, which is clinically applied to treat cancer-induced bone diseases, appears to possess direct anti-tumor activity through apoptosis induction by inhibiting mevalonate pathway and prenylation of intracellular small G proteins. In this study, we evaluated whether ZOL can be effectively used as an adjuvant to TMZ in human malignant glioma cells that express MGMT. Malignant glioma cell lines, in which the expression of MGMT was detected, did not exhibit growth inhibition by TMZ even at a longer exposure. However, combination experiment of TMZ plus ZOL revealed that a supra-additive effect resulted in a significant decrease in cell growth. In combined TMZ/ZOL treatment, an increased apoptotic rate was apparent and significant activation of caspase-3 and cleavage of poly-(ADP-ribose polymerase were observed compared with each single drug exposure. There were decreased amounts of Ras-GTP, MAPK and Akt phosphorylation and MGMT expression in the ZOL-treated cells. Subcutanous xenograft models showed significant decrease of tumor growth with combined TMZ/ZOL treatment. These results suggest that ZOL efficaciously inhibits activity of Ras in malignant glioma cells and potentiates TMZ-mediated cytotoxicity, inducing growth inhibition and apoptosis of malignant glioma cells that express MGMT and resistant to TMZ. Based on this work, combination of TMZ with ZOL might be a potential therapy in malignant gliomas that receive less therapeutic effects of TMZ due to cell resistance.

  6. A Comparative Phase I Study of Combination, Homologous Subtype-C DNA, MVA, and Env gp140 Protein/Adjuvant HIV Vaccines in Two Immunization Regimes (United States)

    Joseph, Sarah; Quinn, Killian; Greenwood, Aldona; Cope, Alethea V.; McKay, Paul F.; Hayes, Peter J.; Kopycinski, Jakub T.; Gilmour, Jill; Miller, Aleisha N.; Geldmacher, Christof; Nadai, Yuka; Ahmed, Mohamed I. M.; Montefiori, David C.; Dally, Len; Bouliotis, George; Lewis, David J. M.; Tatoud, Roger; Wagner, Ralf; Esteban, Mariano; Shattock, Robin J.; McCormack, Sheena; Weber, Jonathan


    There remains an urgent need for a prophylactic HIV vaccine. We compared combined MVA and adjuvanted gp140 to sequential MVA/gp140 after DNA priming. We expected Env-specific CD4+ T-cells after DNA and MVA priming, and Env-binding antibodies in 100% individuals after boosting with gp140 and that combined vaccines would not compromise safety and might augment immunogenicity. Forty volunteers were primed three times with DNA plasmids encoding (CN54) env and (ZM96) gag-pol-nef at 0, 4 and 8 weeks then boosted with MVA-C (CN54 env and gag-pol-nef) and glucopyranosyl lipid adjuvant—aqueous formulation (GLA-AF) adjuvanted CN54gp140. They were randomised to receive them in combination at the same visit at 16 and 20 weeks (accelerated) or sequentially with MVA-C at 16, 20, and GLA-AF/gp140 at 24 and 28 weeks (standard). All vaccinations were intramuscular. Primary outcomes included ≥grade 3 safety events and the titer of CN54gp140-specific binding IgG. Other outcomes included neutralization, binding antibody specificity and T-cell responses. Two participants experienced asymptomatic ≥grade 3 transaminitis leading to discontinuation of vaccinations, and three had grade 3 solicited local or systemic reactions. A total of 100% made anti-CN54gp140 IgG and combining vaccines did not significantly alter the response; geometric mean titer 6424 (accelerated) and 6578 (standard); neutralization of MW965.2 Tier 1 pseudovirus was superior in the standard group (82 versus 45% responders, p = 0.04). T-cell ELISpot responses were CD4+ and Env-dominant; 85 and 82% responding in the accelerated and standard groups, respectively. Vaccine-induced IgG responses targeted multiple regions within gp120 with the V3 region most immunodominant and no differences between groups detected. Combining MVA and gp140 vaccines did not result in increased adverse events and did not significantly impact upon the titer of Env-specific binding antibodies, which were seen in 100% individuals

  7. Evaluation of DNA Extraction Methods for Use in Combination with SYBR Green I Real-Time PCR To Detect Salmonella enterica Serotype Enteritidis in Poultry (United States)

    De Medici, Dario; Croci, Luciana; Delibato, Elisabetta; Di Pasquale, Simona; Filetici, Emma; Toti, Laura


    The objective of this study was to develop a rapid, reproducible, and robust method for detecting Salmonella enterica serotype Enteritidis in poultry samples. First, for the extraction and purification of DNA from the preenrichment culture, four methods (boiling, alkaline lysis, Nucleospin, and Dynabeads DNA Direct System I) were compared. The most effective method was then combined with a real-time PCR method based on the double-stranded DNA binding dye SYBR Green I used with the ABI Prism 7700 system. The specificity of the reaction was determined by the melting temperature (Tm) of the amplicon obtained. The experiments were conducted both on samples of chicken experimentally contaminated with serotype Enteritidis and on commercially available poultry samples, which were also used for comparisons with the standard cultural method (i.e., ISO 6579/2001). The results of comparisons among the four DNA extraction methods showed significant differences except for the results from the boiling and Nucleospin methods (the two methods that produced the lowest threshold cycles). Boiling was selected as the preferred extraction method because it is the simplest and most rapid. This method was then combined with SYBR Green I real-time PCR, using primers SEFA-1 and SEFA-2. The specificity of the reaction was confirmed by the Tm, which was consistently specific for the amplicon obtained; the mean peak Tm obtained with curves specific for serotype Enteritidis was 82.56 ± 0.22°C. The standard curve constructed using the mean threshold cycle and various concentrations of serotype Enteritidis (ranging from 103 to 108 CFU/ml) showed good linearity (R2 = 0.9767) and a sensitivity limit of less than 103 CFU/ml. The results of this study demonstrate that the SYBR Green I real-time PCR constitutes an effective and easy-to-perform method for detecting serotype Enteritidis in poultry samples. PMID:12788750

  8. An epigenetic biomarker combination of PCDH17 and POU4F2 detects bladder cancer accurately by methylation analyses of urine sediment DNA in Han Chinese (United States)

    Li, Qiaoling; An, Dan; Fang, Lu; Lin, Youcheng; Hou, Yong; Xu, Abai; Fu, Yu; Lu, Wei; Chen, Xin; Chen, Mingwei; Zhang, Meng; Jiang, Huiling; Zhang, Chuanxia; Dong, Pei; Li, Chong; Chen, Jun; Yang, Guosheng; Liu, Chunxiao; Cai, Zhiming; Zhou, Fangjian; Wu, Song


    To develop a routine and effectual procedure of detecting bladder cancer (BlCa), an optimized combination of epigenetic biomarkers that work synergistically with high sensitivity and specificity is necessary. In this study, methylation levels of seven biomarkers (EOMES, GDF15, NID2, PCDH17, POU4F2, TCF21, and ZNF154) in 148 individuals—which including 58 urothelial cell carcinoma (UCC) patients, 20 infected urinary calculi (IUC) patients, 20 kidney cancer (KC) patients,20 prostate cancer (PC) patients, and 30 healthy volunteers (HV)—were quantified by qMSP using the urine sediment DNA. Receiver operating characteristic (ROC) curves were generated for each biomarker. The combining predictors of possible combinations were calculated through logistic regression model. Subsequently, ROC curves of the three best performing combinations were constructed. Then, we validated the three best performing combinations and POU4F2 in another 72 UCC, 21 IUC, 26 KC and 22 PC, and 23 HV urine samples. The combination of POU4F2/PCDH17 has yielded the highest sensitivity and specificity of 90.00% and 93.96% in all the 312 individuals, showing the capability of detecting BlCa effectively among pathologically varied sample groups. PMID:26700620

  9. Predictive microbiology combined with metagenomic analysis targeted on the 16S rDNA : A new approach for food quality


    Delhalle, Laurent; Ellouze, Mariem; Taminiau, Bernard; Korsak Koulagenko, Nicolas; Nezer, Carine; Daube,Georges


    OBJECTIVES The food spoilage process is mainly caused by alteration micro-organisms and classical culture-based methods have therefore been used to assess the microbiological quality of food. These techniques are simple to implement but may not be relevant to understand the modifications of the microbial ecology which occur in the food product in response to different changes in the environmental conditions. Metagenomic analysis targeted on 16S ribosomal DNA can bring about a solution to t...

  10. [A novel immunization strategy to induce strong humoral responses against HIV-1 using combined DNA, recombinant vaccinia virus and protein vaccines]. (United States)

    Liu, Chang; Wang, Shu-hui; Ren, Li; Hao, Yan-ling; Zhang, Qi-cheng; Liu, Ying


    To optimize the immunization strategy against HIV-1, a DNA vaccine was combined with a recombinant vaccinia virus (rTV) vaccine and a protein vaccine. Immune responses against HIV-1 were detected in 30 female guinea pigs divided into six groups. Three groups of guinea pigs were primed with HIV-1 DNA vaccine three times, boosted with rTV at week 14, and then boosted with gp140 protein at intervals of 4, 8 or 12 weeks. Simultaneously, the other three groups of animals were primed with rTV vaccine once, and then boosted with gp140 after 4, 8 or 12 weeks. The HIV-1 specific binding antibody and neutralizing antibody, in addition to the relative affinity of these antibodies, were detected at different time points after the final administration of vaccine in each group. The DNA-rTV-gp140 immune regimen induced higher titers and affinity levels of HIV-1 gp120/gp140 antibodies and stronger V1V2-gp70 antibodies than the rTV-gp140 regimen. In the guinea pigs that underwent the DNA-rTV-gp140 regimen, the highest V1V2-gp70 antibody was induced in the 12-week-interval group. However, the avidity of antibodies was improved in the 4-week-interval group. Using the rTV-gp140 immunization strategy, guinea pigs boosted at 8 or 12 weeks after rTV priming elicited stronger humoral responses than those boosted at 4 weeks after priming. In conclusion, this study shows that the immunization strategy of HIV-1 DNA vaccine priming, followed by rTV and protein vaccine boosting, could strengthen the humoral response against HIV-1. Longer intervals were better to induce V1V2-gp70-specific antibodies, while shorter intervals were more beneficial to enhance the avidity of antibodies.

  11. Two splice-factor mutant leukemia subgroups uncovered at the boundaries of MDS and AML using combined gene expression and DNA-methylation profiling. (United States)

    Taskesen, Erdogan; Havermans, Marije; van Lom, Kirsten; Sanders, Mathijs A; van Norden, Yvette; Bindels, Eric; Hoogenboezem, Remco; Reinders, Marcel J T; Figueroa, Maria E; Valk, Peter J M; Löwenberg, Bob; Melnick, Ari; Delwel, Ruud


    Mutations in splice factor (SF) genes occur more frequently in myelodysplastic syndromes (MDS) than in acute myeloid leukemias (AML). We sequenced complementary DNA from bone marrow of 47 refractory anemia with excess blasts (RAEB) patients, 29 AML cases with low marrow blast cell count, and 325 other AML patients and determined the presence of SF-hotspot mutations in SF3B1, U2AF35, and SRSF2. SF mutations were found in 10 RAEB, 12 AML cases with low marrow blast cell count, and 25 other AML cases. Our study provides evidence that SF-mutant RAEB and SF-mutant AML are clinically, cytologically, and molecularly highly similar. An integrated analysis of genomewide messenger RNA (mRNA) expression profiling and DNA-methylation profiling data revealed 2 unique patient clusters highly enriched for SF-mutant RAEB/AML. The combined genomewide mRNA expression profiling/DNA-methylation profiling signatures revealed 1 SF-mutant patient cluster with an erythroid signature. The other SF-mutant patient cluster was enriched for NRAS/KRAS mutations and showed an inferior survival. We conclude that SF-mutant RAEB/AML constitutes a related disorder overriding the artificial separation between AML and MDS, and that SF-mutant RAEB/AML is composed of 2 molecularly and clinically distinct subgroups. We conclude that SF-mutant disorders should be considered as myeloid malignancies that transcend the boundaries of AML and MDS.

  12. DPT tautomerisation of the G·A(syn) and A*·G*(syn) DNA mismatches: a QM/QTAIM combined atomistic investigation. (United States)

    Brovarets', Ol'ha O; Hovorun, Dmytro M


    By applying a combined QM and QTAIM atomistic computational approach we have established for the first time that the G·A(syn) and A*·G*(syn) DNA mismatches (rare tautomers are marked with an asterisk), causing spontaneous transversions with substantially various probabilities, radically differ from each other in their ability to tautomerise through the double proton transfer (DPT). The A*·G*(syn) mismatch tautomerises quite easily (ΔΔG(TS) ≈ 4·kT at room temperature) into the A·G*(syn) mismatch through the asynchronous concerted mechanism, whereas the G·A(syn) base mispair does not tautomerise via the DPT at all, since there is no local minimum corresponding to the tautomerised G*·A*(syn) mismatch on the potential energy surface. It was established that the A·G*(syn) base mispair is a dynamically unstable H-bonded complex with an extremely short lifetime of 2.17 × 10(-13) s. Consequently, the obtained results allow us to believe that spontaneous or forced dissociation of both the G·A(syn) and A*·G*(syn) DNA mismatches by the DNA-polymerase occurs with the preservation of the tautomeric status of the bases.

  13. Targeted silencing of DNA-specific B cells combined with partial plasma cell depletion displays additive effects on delaying disease onset in lupus-prone mice. (United States)

    Nikolova-Ganeva, K A; Gesheva, V V; Todorov, T A; Voll, R E; Vassilev, T L


    Targeting autoreactive B lymphocytes at any stage of their differentiation could yield viable therapeutic strategies for treating autoimmunity. All currently used drugs, including the most recently introduced biological agents, lack target specificity. Selective silencing of double-stranded DNA-specific B cells in animals with spontaneous lupus has been achieved previously by the administration of a chimeric antibody molecule that cross-links their DNA-reactive B cell immunoglobulin receptors with inhibitory FcγIIb (CD32) receptors. However, long-lived plasmacytes are resistant to this chimeric antibody as well as to all conventional treatments. Bortezomib (a proteasome inhibitor) depletes most plasma cells and has been shown recently to suppress disease activity in lupus mice. We hypothesized that the co-administration of non-toxic doses of bortezomib, that partially purge long-lived plasma cells, together with an agent that selectively silences DNA-specific B cells, should have additive effects in an autoantibody-mediated disease. Indeed, our data show that the simultaneous treatment of lupus-prone MRL/lpr mice with suboptimal doses of bortezomib plus the chimeric antibody resulted in the prevention or the delayed appearance of the disease manifestations as well as in a prolonged survival. The effect of the combination therapy was significantly stronger than that of the respective monotherapies and was comparable to that observed after cyclophosphamide administration.

  14. Novel compound heterozygous DNA ligase IV mutations in an adolescent with a slowly-progressing radiosensitive-severe combined immunodeficiency. (United States)

    Tamura, Shinobu; Higuchi, Kohei; Tamaki, Masaharu; Inoue, Chizuko; Awazawa, Ryoko; Mitsuki, Noriko; Nakazawa, Yuka; Mishima, Hiroyuki; Takahashi, Kenzo; Kondo, Osamu; Imai, Kohsuke; Morio, Tomohiro; Ohara, Osamu; Ogi, Tomoo; Furukawa, Fukumi; Inoue, Masami; Yoshiura, Koh-ichiro; Kanazawa, Nobuo


    We herein describe a case of a 17-year-old boy with intractable common warts, short stature, microcephaly and slowly-progressing pancytopenia. Simultaneous quantification of T-cell receptor recombination excision circles (TREC) and immunoglobulin κ-deleting recombination excision circles (KREC) suggested very poor generation of both T-cells and B-cells. By whole exome sequencing, novel compound heterozygous mutations were identified in the patient's DNA ligase IV (LIG4) gene. The diagnosis of LIG4 syndrome was confirmed by delayed DNA double-strand break repair kinetics in γ-irradiated fibroblasts from the patient and their restoration by an introduction of wild-type LIG4. Although the patient received allogeneic hematopoietic stem cell transplantation from his haploidentical mother, he unfortunately expired due to an insufficiently reconstructed immune system. An earlier definitive diagnosis using TREC/KREC quantification and whole exome sequencing would thereby allow earlier intervention, which would be essential for improving long-term survival in similar cases with slowly-progressing LIG4 syndrome masked in adolescents.

  15. Response of arsenic-induced oxidative stress, DNA damage, and metal imbalance to combined administration of DMSA and monoisoamyl-DMSA during chronic arsenic poisoning in rats. (United States)

    Bhadauria, S; Flora, S J S


    Arsenic and its compounds cause adverse health effects in humans. Current treatment employs administration of thiol chelators, such as meso-2,3-dimercaptosuccinic acid (DMSA) and sodium 2,3-dimercaptopropane 1-sulfonate (DMPS), which facilitate its excretion from the body. However, these chelating agents are compromised by number of limitations due to their lipophobic nature, particularly in case of chronic poisoning. Combination therapy is a new approach to ensure enhanced removal of metal from the body, reduced doses of potentially toxic chelators, and no redistribution of metal from one organ to another, following chronic metal exposure. The present study attempts to investigate dose-related effects of two thiol chelators, DMSA and one of its new analogues, monoisoamyl dimercaptosuccinic acid (MiADMSA), when administered in combination with the aim of achieving normalization of altered biochemical parameters suggestive of oxidative stress and depletion of inorganic arsenic following chronic arsenic exposure. Twenty-five adult male Wistar rats were given 25 ppm arsenic for 10 weeks followed by chelation therapy with the above chelating agents at a dose of 0.3 mmol/kg (orally) when administered individually or 0.15 mmol/kg and 0.3 mmol/kg (once daily for 5 consecutive days), respectively, when administered in combination. Arsenic exposure led to the inhibition of blood delta-aminolevulinic acid dehydratase (ALAD) activity and depletion of glutathione (GSH) level. These changes were accompanied by significant depletion of hemoglobin, RBC and Hct as well as blood superoxide dismutase (SOD) acitivity. There was an increase in hepatic and renal levels of thiobarbituric acid-reactive substances, while GSH:GSSG ratio decreased significantly, accompanied by a significant increase in metallothionein (MT) in hepatocytes. DNA damage based on denaturing polyacrylamide gel electrophoresis revealed significant loss in the integrity of DNA extracted from the liver of arsenic

  16. CD40 ligand and tdTomato-armed vaccinia virus for induction of antitumor immune response and tumor imaging. (United States)

    Parviainen, S; Ahonen, M; Diaconu, I; Hirvinen, M; Karttunen, Å; Vähä-Koskela, M; Hemminki, A; Cerullo, V


    Oncolytic vaccinia virus is an attractive platform for immunotherapy. Oncolysis releases tumor antigens and provides co-stimulatory danger signals. However, arming the virus can improve efficacy further. CD40 ligand (CD40L, CD154) can induce apoptosis of tumor cells and it also triggers several immune mechanisms. One of these is a T-helper type 1 (Th1) response that leads to activation of cytotoxic T-cells and reduction of immune suppression. Therefore, we constructed an oncolytic vaccinia virus expressing hCD40L (vvdd-hCD40L-tdTomato), which in addition features a cDNA expressing the tdTomato fluorochrome for detection of virus, potentially important for biosafety evaluation. We show effective expression of functional CD40L both in vitro and in vivo. In a xenograft model of bladder carcinoma sensitive to CD40L treatment, we show that growth of tumors was significantly inhibited by the oncolysis and apoptosis following both intravenous and intratumoral administration. In a CD40-negative model, CD40L expression did not add potency to vaccinia oncolysis. Tumors treated with vvdd-mCD40L-tdtomato showed enhanced efficacy in a syngenic mouse model and induced recruitment of antigen-presenting cells and lymphocytes at the tumor site. In summary, oncolytic vaccinia virus coding for CD40L mediates multiple antitumor effects including oncolysis, apoptosis and induction of Th1 type T-cell responses.

  17. Sensitive Electrochemiluminescence Immunosensor for Detection of N-Acetyl-β-d-glucosaminidase Based on a "Light-Switch" Molecule Combined with DNA Dendrimer. (United States)

    Wang, Haijun; Yuan, Yali; Zhuo, Ying; Chai, Yaqin; Yuan, Ruo


    Here, a novel "light-switch" molecule of Ru (II) complex ([Ru(dcbpy)2dppz](2+)-DPEA) with self-enhanced electrochemiluminescence (ECL) property is proposed, which is almost nonemissive in aqueous solution but is brightly luminescent when it intercalates into DNA duplex. Owing to less energy loss and shorter electron-transfer distance, the intramolecular ECL reaction between the luminescent [Ru(dcbpy)2dppz](2+) and coreactive tertiary amine group in N,N-diisopropylethylenediamine (DPEA) makes the obtained "light-switch" molecule possess much higher light-switch efficiency compared with the traditional "light-switch" molecule. For increasing the loading amount and further enhancing the luminous efficiency of the "light-switch" molecule, biotin labeled DNA dendrimer (the fourth generation, G4) is prepared from Y-shape DNA by a step-by-step assembly strategy, which provides abundant intercalated sites for [Ru(dcbpy)2dppz](2+)-DPEA. Meanwhile, the obtained nanocomposite (G4-[Ru(dcbpy)2dppz](2+)-DPEA) could well bind with streptavidin labeled detection antibody (SA-Ab2) due to the existence of abundant biotin. Through sandwiched immunoreaction, an ECL immunosensor was fabricated for sensitive determination of N-acetyl-β-d-glucosaminidase (NAG), a typical biomarker for diabetic nephropathy (DN). The detemination linear range was 0.1 pg mL(-1) to 1 ng mL(-1), and the detection limit was 0.028 pg mL(-1). The developed strategy combining the ECL self-enhanced "light-switch" molecular and DNA nanotechnology offers an effective signal amplification mean and provides ample potential for further bioanalysis and clinical study.

  18. Removal of Contaminant DNA by Combined UV-EMA Treatment Allows Low Copy Number Detection of Clinically Relevant Bacteria Using Pan-Bacterial Real-Time PCR.

    Directory of Open Access Journals (Sweden)

    Bruce Humphrey

    Full Text Available More than two decades after its discovery, contaminant microbial DNA in PCR reagents continues to impact the sensitivity and integrity of broad-range PCR diagnostic techniques. This is particularly relevant to their use in the setting of human sepsis, where a successful diagnostic on blood samples needs to combine universal bacterial detection with sensitivity to 1-2 genome copies, because low levels of a broad range of bacteria are implicated.We investigated the efficacy of ethidium monoazide (EMA and propidium monoazide (PMA treatment as emerging methods for the decontamination of PCR reagents. Both treatments were able to inactivate contaminating microbial DNA but only at concentrations that considerably affected assay sensitivity. Increasing amplicon length improved EMA/PMA decontamination efficiency but at the cost of assay sensitivity. The same was true for UV exposure as an alternative decontamination strategy, likely due to damage sustained by oligonucleotide primers which were a significant source of contamination. However, a simple combination strategy with UV-treated PCR reagents paired with EMA-treated primers produced an assay capable of two genome copy detection and a <5% contamination rate. This decontamination strategy could have important utility in developing improved pan-bacterial assays for rapid diagnosis of low pathogen burden conditions such as in the blood of patients with suspected blood stream infection.

  19. Phylogenetic relationships among the microgastroid wasps (Hymenoptera: braconidae): combined analysis of 16S and 28S rDNA genes and morphological data. (United States)

    Dowton, M; Austin, A D


    Relationships among the microgastroid complex of braconid wasps were investigated using sequence data from the 16S mitochondrial rDNA and 28S (D2 expansion region) nuclear rDNA genes, as well as morphological data. Parsimony analysis of these gene fragments, both separately and combined, indicated that Neoneurus (Neoneurinae) and Ichneutes (Ichneutinae) were no more closely related to the microgastroids than were a range of helconoid taxa. Combined parsimony analysis of the microgastroids indicated the relationships ((Cardiochilinae + Microgastrinae) + Miracinae) + Cheloninae, with Adeliinae falling inside the Cheloninae. Bootstrap proportions for each of these nodes were greater than 70%. Character reweighting (sensu Farris), using the rescaled consistency index, also recovered these relationships. Mapping of lifestyle traits onto this relatively well supported phylogeny indicated that solitary endoparasitism is ancestral for the microgastroids, with a single origin for egg-larval endoparasitism in the Cheloninae + Adeliinae. Mapping of the radiation of the microgastroids into lepidopteran hosts was less clear, due to the specialized biology of the most basal microgastroid clade, the Cheloninae + Adeliinae. Our data are consistent with attack of concealed lepidopteran hosts as the plesiomorphic lifestyle, at least for the Miracinae + Cardiochilinae + Microgastrinae, with radiation into more exposed hosts in the Cardiochilinae + Microgastrinae.

  20. DNA immunization combined with scFv phage display identifies antagonistic GCGR specific antibodies and reveals new epitopes on the small extracellular loops. (United States)

    van der Woning, Bas; De Boeck, Gitte; Blanchetot, Christophe; Bobkov, Vladimir; Klarenbeek, Alex; Saunders, Michael; Waelbroeck, Magali; Laeremans, Toon; Steyaert, Jan; Hultberg, Anna; De Haard, Hans


    The identification of functional monoclonal antibodies directed against G-protein coupled receptors (GPCRs) is challenging because of the membrane-embedded topology of these molecules. Here, we report the successful combination of llama DNA immunization with scFv-phage display and selections using virus-like particles (VLP) and the recombinant extracellular domain of the GPCR glucagon receptor (GCGR), resulting in glucagon receptor-specific antagonistic antibodies. By immunizing outbred llamas with plasmid DNA containing the human GCGR gene, we sought to provoke their immune system, which generated a high IgG1 response. Phage selections on VLPs allowed the identification of mAbs against the extracellular loop regions (ECL) of GCGR, in addition to multiple VH families interacting with the extracellular domain (ECD) of GCGR. Identifying mAbs binding to the ECL regions of GCGR is challenging because the large ECD covers the small ECLs in the energetically most favorable 'closed conformation' of GCGR. Comparison of Fab with scFv-phage display demonstrated that the multivalent nature of scFv display is essential for the identification of GCGR specific clones by selections on VLPs because of avid interaction. Ten different VH families that bound 5 different epitopes on the ECD of GCGR were derived from only 2 DNA-immunized llamas. Seven VH families demonstrated interference with glucagon-mediated cAMP increase. This combination of technologies proved applicable in identifying multiple functional binders in the class B GPCR context, suggesting it is a robust approach for tackling difficult membrane proteins.

  1. Genomic comparison of Yersinia pestis and Yersinia pseudotuberculosis by combination of suppression subtractive hybridization and DNA microarray

    DEFF Research Database (Denmark)

    Wang, Xiaoyi; Zhou, Dongsheng; Qin, Long


    a combination of suppression subtractive hybridization (SSH) and comparative genomic hybridization with DNAs from a diverse panel of Y. pestis and Y. pseudotuberculosis strains. SSH followed by BLAST analysis revealed 112 SSH fragments specific to strain ATCC29833, compared to the genomic sequence data of Y....... pestis strains CO92, KIM and 91001. We identified 17 SSH fragments that appeared to be newly determined genetic contents of Y. pseudotuberculosis. The combination of SSH and microarray analysis showed that the parallel loss of genes contributed greatly not only to the significant genomic divergence...

  2. A Combined Computational and Experimental Study on the Structure-Regulation Relationships of Putative Mammalian DNA Replication Initiator GINS

    Institute of Scientific and Technical Information of China (English)

    Reiko Hayashi; Takako Arauchi; Moe Tategu; Yuya Goto; Kenichi Yoshida


    GINS, a heterotetramer of SLD5, PSF1, PSF2, and PSF3 proteins, is an emerging chromatin factor recognized to be involved in the initiation and elongation step of DNA replication. Although the yeast and Xenopus GINS genes are well documented, their orthologous genes in higher eukaryotes are not fully characterized.In this study, we report the genomic structure and transcriptional regulation of mammalian GINS genes. Serum stimulation increased the GINS Mrna levels in human cells. Reporter gene assay using putative GINS promoter sequences revealed that the expression of mammalian GINS is regulated by 17β-Estradiolstimulated estrogen receptor α, and human PSF3 acts as a gene responsive to transcription factor E2F1. The goal of this study is to present the current data so as to encourage further work in the field of GINS gene regulation and functions in mammalian cells.

  3. A rapid and versatile combined DNA/RNA extraction protocol and its application to the analysis of a novel DNA marker set polymorphic between Arabidopsis thaliana ecotypes Col-0 and Landsberg erecta

    Directory of Open Access Journals (Sweden)

    Coupland George


    Full Text Available Abstract Background Many established PCR-based approaches in plant molecular biology rely on lengthy and expensive methods for isolation of nucleic acids. Although several rapid DNA isolation protocols are available, they have not been tested for simultaneous RNA isolation for RT-PCR applications. In addition, traditional map-based cloning technologies often use ill-proportioned marker regions even when working with the model plant Arabidopsis thaliana, where the availability of the full genome sequence can now be exploited for the creation of a high-density marker systems. Results We designed a high-density polymorphic marker set between two frequently used ecotypes. This new polymorphic marker set allows size separation of PCR products on agarose gels and provides an initial resolution of 10 cM in linkage mapping experiments, facilitated by a rapid plant nucleic acid extraction protocol using minimal amounts of A. thaliana tissue. Using this extraction protocol, we have also characterized segregating T-DNA insertion mutations. In addition, we have shown that our rapid nucleic acid extraction protocol can also be used for monitoring transcript levels by RT-PCR amplification. Finally we have demonstrated that our nucleic acid isolation method is also suitable for other plant species, such as tobacco and barley. Conclusion To facilitate high-throughput linkage mapping and other genomic applications, our nucleic acid isolation protocol yields sufficient quality of DNA and RNA templates for PCR and RT-PCR reactions, respectively. This new technique requires considerably less time compared to other purification methods, and in combination with a new polymorphic PCR marker set dramatically reduces the workload required for linkage mapping of mutations in A. thaliana utilizing crosses between Col-0 and Landsberg erecta (Ler ecotypes.

  4. Rapid Classification of Turmeric Based on DNA Fingerprint by Near-Infrared Spectroscopy Combined with Moving Window Partial Least Squares-Discrimination Analysis. (United States)

    Kasemsumran, Sumaporn; Suttiwijitpukdee, Nattaporn; Keeratinijakal, Vichein


    In this research, near-infrared (NIR) spectroscopy in combination with moving window partial least squares-discrimination analysis (MWPLS-DA) was utilized to discriminate the variety of turmeric based on DNA markers, which correlated to the quantity of curcuminoid. Curcuminoid was used as a marker compound in variety identification due to the most pharmacological properties of turmeric possessed from it. MWPLS-DA optimized informative NIR spectral regions for the fitting and prediction to {-1/1}-coded turmeric varieties, indicating variables in the development of latent variables in discrimination analysis. Consequently, MWPLS-DA benefited in the selection of combined informative NIR spectral regions of 1100 - 1260, 1300 - 1500 and 1880 - 2500 nm for classification modeling of turmeric variety with 148 calibration samples, and yielded the results better than that obtained from a partial least squares-discrimination analysis (PLS-DA) model built by using the whole NIR spectral region. An effective and rapid strategy of using NIR in combination with MWPLS-DA provided the best variety identification results of 100% in both specificity and total accuracy for 48 test samples.

  5. Combining real-time PCR and next-generation DNA sequencing to provide quantitative comparisons of fungal aerosol populations (United States)

    Dannemiller, Karen C.; Lang-Yona, Naama; Yamamoto, Naomichi; Rudich, Yinon; Peccia, Jordan


    We examined fungal communities associated with the PM10 mass of Rehovot, Israel outdoor air samples collected in the spring and fall seasons. Fungal communities were described by 454 pyrosequencing of the internal transcribed spacer (ITS) region of the fungal ribosomal RNA encoding gene. To allow for a more quantitative comparison of fungal exposure in humans, the relative abundance values of specific taxa were transformed to absolute concentrations through multiplying these values by the sample's total fungal spore concentration (derived from universal fungal qPCR). Next, the sequencing-based absolute concentrations for Alternaria alternata, Cladosporium cladosporioides, Epicoccum nigrum, and Penicillium/Aspergillus spp. were compared to taxon-specific qPCR concentrations for A. alternata, C. cladosporioides, E. nigrum, and Penicillium/Aspergillus spp. derived from the same spring and fall aerosol samples. Results of these comparisons showed that the absolute concentration values generated from pyrosequencing were strongly associated with the concentration values derived from taxon-specific qPCR (for all four species, p 0.70). The correlation coefficients were greater for species present in higher concentrations. Our microbial aerosol population analyses demonstrated that fungal diversity (number of fungal operational taxonomic units) was higher in the spring compared to the fall (p = 0.02), and principal coordinate analysis showed distinct seasonal differences in taxa distribution (ANOSIM p = 0.004). Among genera containing allergenic and/or pathogenic species, the absolute concentrations of Alternaria, Aspergillus, Fusarium, and Cladosporium were greater in the fall, while Cryptococcus, Penicillium, and Ulocladium concentrations were greater in the spring. The transformation of pyrosequencing fungal population relative abundance data to absolute concentrations can improve next-generation DNA sequencing-based quantitative aerosol exposure assessment.

  6. DNA nanostructure immobilization to lithographic DNA arrays (United States)

    Negrete, Omar D.

    Although DNA is well known for its genetic role in biology, DNA has also been sought-after as a material for the self-assembly of biological and electronic devices. Examples of DNA nanostructure construction include DNA tiled self-assembly and DNA Origami, where by controlling the sequence and concentration of DNA molecules, the rational design of geometric DNA nanostructures is possible. The assembly of DNA nanostructures takes place in solution and thus they are in disorder and require further organization to construct circuitry or devices. Hence, it is essential for future applications of this technology to develop methods to direct the placement of DNA nanostructures on a surface. To address this challenge my research examines the use of DNA microarrays to capture DNA nanostructures via DNA hybridization. Modern DNA arrays offer a high-density of sequence-specific molecular recognition sites where the addressable placement of DNA nanostructures can be achieved. Using Maskless Array Synthesizer (MAS) technology, I have characterized photolithographic DNA arrays for the hybridization of DNA complexes like large DNA molecules (> 1 kb), DNA-gold nanoparticle conjugates, and DNA Origami. Although modern photolithographic DNA arrays can possess a high-density of sequence (106/cm2), the printed DNA areas are on the order of tens of microns. Thus, I have also developed a method to reduce the DNA array spot size to nanoscale dimensions through the combined use of electron beam lithography with photolithographic DNA synthesis. This work addresses the key elements towards developing a surface patterning technology that takes advantage of DNA base-pairing for both molecular sub-assembly and surface patterning.

  7. Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping (United States)

    Müller, Vilhelm; Rajer, Fredrika; Frykholm, Karolin; Nyberg, Lena K.; Quaderi, Saair; Fritzsche, Joachim; Kristiansson, Erik; Ambjörnsson, Tobias; Sandegren, Linus; Westerlund, Fredrik


    Bacterial plasmids are extensively involved in the rapid global spread of antibiotic resistance. We here present an assay, based on optical DNA mapping of single plasmids in nanofluidic channels, which provides detailed information about the plasmids present in a bacterial isolate. In a single experiment, we obtain the number of different plasmids in the sample, the size of each plasmid, an optical barcode that can be used to identify and trace the plasmid of interest and information about which plasmid that carries a specific resistance gene. Gene identification is done using CRISPR/Cas9 loaded with a guide-RNA (gRNA) complementary to the gene of interest that linearizes the circular plasmids at a specific location that is identified using the optical DNA maps. We demonstrate the principle on clinically relevant extended spectrum beta-lactamase (ESBL) producing isolates. We discuss how the gRNA sequence can be varied to obtain the desired information. The gRNA can either be very specific to identify a homogeneous group of genes or general to detect several groups of genes at the same time. Finally, we demonstrate an example where we use a combination of two gRNA sequences to identify carbapenemase-encoding genes in two previously not characterized clinical bacterial samples.

  8. Combination of treatment with death receptor 5-specific antibody with therapeutic HPV DNA vaccination generates enhanced therapeutic anti-tumor effects. (United States)

    Tseng, Chih Wen; Monie, Archana; Trimble, Cornelia; Alvarez, Ronald D; Huh, Warner K; Buchsbaum, Donald J; Straughn, J Michael; Wang, Mei-Cheng; Yagita, Hideo; Hung, Chien-Fu; Wu, T-C


    There is currently a vital need for the development of novel therapeutic strategies for the control of advanced stage cancers. Antigen-specific immunotherapy and the employment of antibodies against the death receptor 5 (DR5) have emerged as two potentially promising strategies for cancer treatment. In the current study, we hypothesize that the combination of treatment with the anti-DR5 monoclonal antibody, MD5-1 with a DNA vaccine encoding calreticulin (CRT) linked to human papillomavirus type 16 (HPV-16) E7 antigen (CRT/E7(detox)) administered via gene gun would lead to further enhancement of E7-specific immune responses as well as anti-tumor effects. Our results indicated that mice bearing the E7-expressing tumor, TC-1 treated with MD5-1 monoclonal antibody followed by CRT/E7(detox) DNA vaccination generated the most potent therapeutic anti-tumor effects as well as highest levels of E7-specific CD8+ T cells among all the groups tested. In addition, treatment with MD5-1 monoclonal antibody was capable of rendering the TC-1 tumor cells more susceptible to lysis by E7-specific cytotoxic T lymphocytes. Our findings serve as an important foundation for future clinical translation.

  9. Double labelling of tissue combining tritiated thymidine autoradiography with immunodetection of bromodeoxyuridine: the autoradiographic significance of inhibition of thymidine incorporation into DNA by bromodeoxyuridine given simultaneously

    Energy Technology Data Exchange (ETDEWEB)

    Hume, W.J.; Thompson, J. (Leeds Univ. (UK). School of Dentistry)


    The authors describe a method for combining tritiated thymidine (({sup 3}H)TdR) autoradiography with immunoperoxidase detection of bromodeoxyuridine (BrdU) in paraffin-embedded tissues, which was used to examine, in mouse tongue epithelium, the inhibition of incorporation into DNA of ({sup 3}H)TdR by simultaneous injection of BrdU in the doses that both compounds are likely to be used in cell proliferation studies. The inhibition of uptake into DNA of ({sup 3}H)TdR from 0.23 to 1.85 MBq (6.25 to 50 {mu}Ci) per animal, produced by a simultaneous injection of 2.5 mg BrdU shows a linear, dose-dependent relationship. Provided the injected dose (in {mu}Ci per animal) multiplied by the autoradiographic exposure time (in days) is greater than a value of 700, then all cells that are labelled after incorporation of ({sup 3}H)TdR alone are also labelled after simultaneous double labelling, despite the latter producing a lower average grain count. (author).

  10. Allelic frequency distributions of 21 non-combined DNA index system STR loci in a Russian ethnic minority group from Inner Mongolia, China* (United States)

    Wang, Hong-dan; Shen, Chun-mei; Liu, Wen-juan; Zhang, Yu-dang; Yang, Guang; Yan, Jiang-wei; Qin, Hai-xia; Zhu, Bo-feng


    We studied the allelic frequency distributions and statistical forensic parameters of 21 new short tandem repeat (STR) loci and the amelogenin locus, which are not included in the combined DNA index system (CODIS), in a Russian ethnic minority group from the Inner Mongolia Autonomous Region, China. A total of 114 bloodstain samples from unrelated individuals were extracted and co-amplified with four fluorescence-labeled primers in a multiplex polymerase chain reaction (PCR) system. Using capillary electrophoresis, the PCR products of the 21 STR loci were separated and genotyped. A total of 161 alleles were observed in the Russian ethnic minority group, and corresponding allelic frequencies ranged from 0.0044 to 0.5965. The 21 non-CODIS STR loci of the Russian ethnic minority group were characterized by high genetic diversity and therefore may be useful for elucidating the population’s genetic background, for individual identification, and for paternity testing in forensic practice. PMID:23733431

  11. Allelic frequency distributions of 21 non-combined DNA index system STR loci in a Russian ethnic minority group from Inner Mongolia, China. (United States)

    Wang, Hong-dan; Shen, Chun-mei; Liu, Wen-juan; Zhang, Yu-dang; Yang, Guang; Yan, Jiang-wei; Qin, Hai-xia; Zhu, Bo-feng


    We studied the allelic frequency distributions and statistical forensic parameters of 21 new short tandem repeat (STR) loci and the amelogenin locus, which are not included in the combined DNA index system (CODIS), in a Russian ethnic minority group from the Inner Mongolia Autonomous Region, China. A total of 114 bloodstain samples from unrelated individuals were extracted and co-amplified with four fluorescence-labeled primers in a multiplex polymerase chain reaction (PCR) system. Using capillary electrophoresis, the PCR products of the 21 STR loci were separated and genotyped. A total of 161 alleles were observed in the Russian ethnic minority group, and corresponding allelic frequencies ranged from 0.0044 to 0.5965. The 21 non-CODIS STR loci of the Russian ethnic minority group were characterized by high genetic diversity and therefore may be useful for elucidating the population's genetic background, for individual identification, and for paternity testing in forensic practice.

  12. Combination of DNA ligase reaction and gold nanoparticle-quenched fluorescent oligonucleotides: a simple and efficient approach for fluorescent assaying of single-nucleotide polymorphisms. (United States)

    Wang, Hao; Li, Jishan; Wang, Yongxiang; Jin, Jiangyu; Yang, Ronghua; Wang, Kemin; Tan, Weihong


    A new fluorescent sensing approach for detection of single-nucleotide polymorphisms (SNPs) is proposed based on the ligase reaction and gold nanoparticle (AuNPs)-quenched fluorescent oligonucleotides. The design exploits the strong fluorescence quenching of AuNPs for organic dyes and the difference in noncovalent interactions of the nanoparticles with single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), where ssDNA can be adsorbed onto the surface of AuNPs while dsDNA cannot be. In the assay, two half primer DNA probes, one being labeled with a dye and the other being phosphorylated, were first incubated with a target DNA template. In the presence of DNA ligase, the two captured ssDNAs are linked for the perfectly matched DNA target to form a stable duplex, but the duplex could not be formed by the single-base mismatched DNA template. After addition of AuNPs, the fluorescence of dye-tagged DNA probe will be efficiently quenched unless the perfectly matched DNA target is present. To demonstrate the feasibility of this design, the performance of SNP detection using two different DNA ligases, T4 DNA ligase and Escherichia coli DNA ligase, were investigated. In the case of T4 DNA ligase, the signal enhancement of the dye-tagged DNA for perfectly matched DNA target is 4.6-fold higher than that for the single-base mismatched DNA. While in the presence of E. coli DNA ligase, the value raises to be 30.2, suggesting excellent capability for SNP discrimination.

  13. Phylogenetic relationships of Middle American cichlids (Cichlidae, Heroini) based on combined evidence from nuclear genes, mtDNA, and morphology. (United States)

    Rícan, Oldrich; Zardoya, Rafael; Doadrio, Ignacio


    Heroine cichlids are the second largest and very diverse tribe of Neotropical cichlids, and the only cichlid group that inhabits Mesoamerica. The taxonomy of heroines is complex because monophyly of most genera has never been demonstrated, and many species groups are without applicable generic names after their removal from the catch-all genus Cichlasoma (sensu Regan, 1905). Hence, a robust phylogeny for the group is largely wanting. A rather complete heroine phylogeny based on cytb sequence data is available [Concheiro Pérez, G.A., Rícan O., Ortí G., Bermingham, E., Doadrio, I., Zardoya, R. 2007. Phylogeny and biogeography of 91 species of heroine cichlids (Teleostei: Cichlidae) based on sequences of the cytochrome b gene. Mol. Phylogenet. Evol. 43, 91-110], and in the present study, we have added and analyzed independent data sets (nuclear and morphological) to further confirm and strengthen the cytb-phylogenetic hypothesis. We have analyzed a combined cytb-nuclear (RAG1 and two S7 introns) data set of 48 species representing main heroine lineages to achieve further resolution of heroine higher taxonomic levels and a combined cytb-morphological data set of 92 species to stabilize generic taxonomy. The recovered phylogenies supported the circumamazonian--CAM--Heroini (sensu Concheiro Peréz et al., 2007) as a monophyletic group, that could be divided into six main clades: (1) australoheroines (the southernmost heroine genus Australoheros), (2) nandopsines (the Antillean genus Nandopsis), (3) caquetaines (including the north western Amazonian genera Caquetaia and Heroina), (4) astatheroines (including Astatheros, Herotilapia and Rocio), (5) amphilophines (including Amphilophus and related genera), and (6) herichthyines (including Herichthyis and related genera). Nuclear and mitochondrial data partitions arrived at highly congruent topologies. Suprageneric relationships were influenced mainly by the nuclear signal, as well as the most basal phylogenetic position

  14. Absence of DNA damage after 60-Hz electromagnetic field exposure combined with ionizing radiation, hydrogen peroxide, or c-Myc overexpression. (United States)

    Jin, Yeung Bae; Choi, Seo-Hyun; Lee, Jae Seon; Kim, Jae-Kyung; Lee, Ju-Woon; Hong, Seung-Cheol; Myung, Sung Ho; Lee, Yun-Sil


    The principal objective of this study was to assess the DNA damage in a normal cell line system after exposure to 60 Hz of extremely low frequency magnetic field (ELF-MF) and particularly in combination with various external factors, via comet assays. NIH3T3 mouse fibroblast cells, WI-38 human lung fibroblast cells, L132 human lung epithelial cells, and MCF10A human mammary gland epithelial cells were exposed for 4 or 16 h to a 60-Hz, 1 mT uniform magnetic field in the presence or absence of ionizing radiation (IR, 1 Gy), H(2)O(2) (50 μM), or c-Myc oncogenic activation. The results obtained showed no significant differences between the cells exposed to ELF-MF alone and the unexposed cells. Moreover, no synergistic or additive effects were observed after 4 or 16 h of pre-exposure to 1 mT ELF-MF or simultaneous exposure to ELF-MF combined with IR, H(2)O(2), or c-Myc activation.

  15. A combined atomic force microscopy imaging and docking study to investigate the complex between p53 DNA binding domain and Azurin. (United States)

    Bizzarri, Anna Rita; Di Agostino, Silvia; Andolfi, Laura; Cannistraro, Salvatore


    The tumor suppressor p53 interacts with the redox copper protein Azurin (AZ) forming a complex which is of some relevance in biomedicine and cancer therapy. To obtain information on the spatial organization of this complex when it is immobilized on a substrate, we have used tapping mode-atomic force microscopy (TM-AFM) imaging combined with computational docking. The vertical dimension and the bearing volume of the DNA binding domain (DBD) of p53, anchored to functionalized gold substrate through exposed lysine residues, alone and after deposing AZ, have been measured by TM-AFM. By a computational docking approach, a three-dimensional model for the DBD of p53, before and after addition of AZ, have been predicted. Then we have calculated the possible arrangements of these biomolecular systems on gold substrate by finding a good agreement with the related experimental distribution of the height. The potentiality of the approach combining TM-AFM imaging and computational docking for the study of biomolecular complexes immobilized on substrates is briefly discussed.

  16. Predicted sub-populations in a marine shrimp proteome as revealed by combined EST and cDNA data from multiple Penaeus species

    Directory of Open Access Journals (Sweden)

    Kotewong Rattanawadee


    Full Text Available Abstract Background Many species of marine shrimp in the Family Penaeidae, viz. Penaeus (Litopenaeus vannamei, Penaeus monodon, Penaeus (Fenneropenaeus chinensis, and Penaeus (Marsupenaeus japonicus, are animals of economic importance in the aquaculture industry. Yet information about their DNA and protein sequences is lacking. In order to predict their collective proteome, we combined over 270,000 available EST and cDNA sequences from the 4 shrimp species with all protein sequences of Drosophila melanogaster and Caenorhabditis elegans. EST data from 4 other crustaceans, the crab Carcinus maenas, the lobster Homarus americanus (Decapoda, the water flea Daphnia pulex, and the brine shrimp Artemia franciscana were also used. Findings Similarity searches from EST collections of the 4 shrimp species matched 64% of the protein sequences of the fruit fly, but only 45% of nematode proteins, indicating that the shrimp proteome content is more similar to that of an insect than a nematode. Combined results with 4 additional non-shrimp crustaceans increased matching to 78% of fruit fly and 56% of nematode proteins, suggesting that present shrimp EST collections still lack sequences for many conserved crustacean proteins. Analysis of matching data revealed the presence of 4 EST groups from shrimp, namely sequences for proteins that are both fruit fly-like and nematode-like, fruit fly-like only, nematode-like only, and non-matching. Gene ontology profiles of proteins for the 3 matching EST groups were analyzed. For non-matching ESTs, a small fraction matched protein sequences from other species in the UniProt database, including other crustacean-specific proteins. Conclusions Shrimp ESTs indicated that the shrimp proteome is comprised of sub-populations of proteins similar to those common to both insect and nematode models, those present specifically in either model, or neither. Combining small EST collections from related species to compensate for their

  17. Establishment and Identification of Chinese Hamster Ovary Cell Lines with Stable Expression of Soluble CD40 Ligands

    Directory of Open Access Journals (Sweden)

    JIANG Hua-wei


    Full Text Available Objective: To establish the Chinese Hamster Ovary (CHO cell lines with stable expression of soluble CD40 ligands (sCD40L. Methods: Recombinant plasmid pIRES2-EGFP-sCD40L, enzyme digestion and sequencing identification were obtained by cloning sCD40L coding sequences into eukaryotic expression vector pIRES2-EGFP from carrier pDC316-sCD40 containing sCD40L. CHO cells were transfected by electroporation, followed by screening of resistant clones with G418, after which monoclones were obtained by limited dilution assay and multiply cultured. Flow cytometer and reverted fluorescence microscope were applied to observe the expression of green fluorescent protein, while sCD40L expression was detected by polymerase chain reaction (PCR, reverse transcription-polymerase chain reaction (RT-PCR and enzyme-linked immunosorbent assay (ELISA from aspects of deoxyribose nucleic acid (DNA, messenger ribonucleic acid (mRNA and protein, respectively. CHO-sCD40L was cultured together with MDA-MB-231 cells to compare the expression changes of surface molecule fatty acid synthase (Fas by flow cytometer and observe the apoptosis of MDA-MB-231 cells after Fas activated antibodies (CH-11 were added 24 h later. Results: Plasmid pIRES2-EGFP-sCD40L was successfully established, and cell lines with stable expression of sCD40L were obtained with cloned culture after CHO cell transfection, which was named as B11. Flow cytometer and reverted fluorescence microscope showed >90% expression of green fluorescent protein, while PCR, RT-PCR and ELISA suggested integration of sCD40L genes into cell genome DNA, transcription of sCD40L mRNA and sCD40L protein expression being (4.5±2.1 ng/mL in the supernatant of cell culture, respectively. After co-culture of B11 and MDA-MB-231 cells, the surface Fas expression of MDA-MB-231 cells was increased from (3±1.02 % to (34.8±8.75%, while the apoptosis rate 24 h after addition of CH11 from (5.4±1.32% to (20.7±5.24%, and the differences

  18. Construction of recombinant eukaryotic expression plasmid containing murine CD40 ligand gene and its expression in H22 cells

    Institute of Scientific and Technical Information of China (English)

    Yong-Fang Jiang; Yan He; Guo-Zhong Gong; Jun Chen; Chun-Yan Yang; Yun Xu


    AIM: To construct a recombinant murine CD40 ligand (mCD40L) eukaryotic expression vector for gene therapy and target therapy of hepatocellular carcinoma (HCC).METHODS: mCD40L cDNA was synthesized by RT-PCR with the specific primers and directly cloned into T vector to generate middle recombinant. After digestion with restriction endonuclease, the target fragment was subcloned into the multi-clone sites of the eukaryotic vector. The constructed vector was verified by enzyme digestion and sequencing,and the product expressed was detected by RT-PCR and immunofluorescence methods.RESULTS: The full-length mCD40L-cDNA was successfully cloned into the eukaryotic vector through electrophoresis,and mCD40L gene was integrated into the genome of infected H22 cells by RT-PCR. Murine CD40L antigen molecule was observed in the plasma of mCD40L-H22 by indirect immuno-fluorescence staining.CONCLUSION: The recombined mCD40L eukaryotic expression vector can be expressed in H22 cell line. It providesexperimental data for gene therapy and target therapy ofhepatocellular carcinoma.

  19. A micro-extraction technique using a new digitally controlled syringe combined with UHPLC for assessment of urinary biomarkers of oxidatively damaged DNA.

    Directory of Open Access Journals (Sweden)

    Berta Mendes

    and the high sensitivity, reproducibility, and robustness of eVol(®MEPS combined with UHPLC analysis, thus retrieving a fast and reliable assessment of oxidatively damaged DNA.

  20. A micro-extraction technique using a new digitally controlled syringe combined with UHPLC for assessment of urinary biomarkers of oxidatively damaged DNA. (United States)

    Mendes, Berta; Silva, Pedro; Aveiro, Fernando; Pereira, Jorge; Câmara, José S


    and the high sensitivity, reproducibility, and robustness of eVol(®)MEPS combined with UHPLC analysis, thus retrieving a fast and reliable assessment of oxidatively damaged DNA.

  1. Molecular cloning, sequencing, and expression analysis of cDNA encoding metalloprotein II (MP II) induced by single and combined metals (Cu(II), Cd(II)) in polychaeta Perinereis aibuhitensis. (United States)

    Yang, Dazuo; Zhou, Yibing; Zhao, Huan; Zhou, Xiaoxiao; Sun, Na; Wang, Bin; Yuan, Xiutang


    We amplified and analyzed the complete cDNA of metalloprotein II (MP II) from the somatic muscle of the polychaete Perinereis aibuhitensis, the full length cDNA is 904 bp encoding 119 amino acids. The MP II cDNA sequence was subjected to BLAST searching in NCBI and was found to share high homology with hemerythrin of other worms. MP II expression of P. aibuhitensis exposed to single and combined metals (Cu(II), Cd(II)) was analyzed using real time-PCR. MP II mRNA expression increased at the start of Cu(II) exposure, then decreased and finally return to the normal level. Expression pattern of MP II under Cd(II) exposure was time- and dose-dependent. MP II expression induced by a combination of Cd(II) and Cu(II) was similar to that induced by Cd(II) alone.

  2. Cationic lipid/DNA complexes (JVRS-100) combined with influenza vaccine (Fluzone) increases antibody response, cellular immunity, and antigenically drifted protection. (United States)

    Lay, Marla; Callejo, Bernadette; Chang, Stella; Hong, David K; Lewis, David B; Carroll, Timothy D; Matzinger, Shannon; Fritts, Linda; Miller, Christopher J; Warner, John F; Liang, Lily; Fairman, Jeffery


    Safe and effective adjuvants for influenza vaccines that could increase both the levels of neutralizing antibody, including against drifted viral subtypes, and T-cell immunity would be a major advance in vaccine design. The JVRS-100 adjuvant, consisting of DOTIM/cholesterol cationic liposome-DNA complexes, is particularly promising for vaccines that require induction of high levels of antibody and T-cell immunity, including CD8(+) cytotoxic T lymphocytes (CTL). Inclusion of protein antigens with JVRS-100 results in the induction of enhanced humoral and cell-mediated (i.e., CD4(+) and CD8(+) T cells) immune responses. The JVRS-100 adjuvant combined with a split trivalent influenza vaccine (Fluzone-sanofi pasteur) elicited increased antibody and T-cell responses in mice and non-human primates compared to vaccination with Fluzone alone. Mice vaccinated with JVRS-100-Fluzone and challenged with antigenically drifted strains of H1N1 (PR/8/34) and influenza B (B/Lee/40) viruses had higher grade protection, as measured by attenuation of weight loss and increased survival, compared to recipients of unadjuvanted vaccine. The results indicate that the JVRS-100 adjuvant substantially increases immunogenicity and protection from drifted-strain challenge using an existing influenza vaccine.

  3. Allele frequencies of combined DNA index system (CODIS) and non-CODIS short tandem repeat loci in Goiás, Central Brazil. (United States)

    Rodovalho, R G; Santos, G S; Cavalcanti, L M; Moura, B F S M; Rodrigues, E L; Lima, P R; Gigonzac, M A D; Vieira, T C


    In studies of human identification, obtaining a high standard of outcomes and satisfactory conclusions are directly related to the use of highly polymorphic molecular markers. In addition to the combined DNA index system (CODIS) group, it is also important to implement non-CODIS markers into the analysis, as they increase the power of discrimination. During the identification process, it is essential to consider the genetic variation among distinct groups of populations, as the allele frequencies are directly associated with the power of discrimination. However, the population of Goiás, a State located in Central Brazil, is characterized by a highly mixed population due to its diverse ethnic origins. In this study, a survey of the allelic frequencies in the Goiás population was carried out using a molecular assembly composed of 21 autosomal loci both from and external to the CODIS group. The new data, for some of the markers used, were statistically similar to those from previous studies. This consistency means that the use of these markers might serve as a parameter for future population comparisons. The results from these analyses further our knowledge of the study of human identification.

  4. Allelic frequency distributions of 21 non-combined DNA index system STR loci in a Russian ethnic minority group from Inner Mongolia, China

    Institute of Scientific and Technical Information of China (English)

    Hong-dan WANG; Chun-mei SHEN; Wen-juan LIU; Yu-dang ZHANG; Guang YANG; Jiang-wei YAN; Hai-xia QIN


    We studied the allelic frequency distributions and statistical forensic parameters of 21 new short tandem repeat (STR) loci and the amelogenin locus,which are not included in the combined DNA index system (CODIS),in a Russian ethnic minority group from the Inner Mongolia Autonomous Region,China.A total of 114 bloodstain samples from unrelated individuals were extracted and co-amplified with four fluorescence-labeled primers in a multiplex polymerase chain reaction (PCR) system.Using capillary electrophoresis,the PCR products of the 21 STR loci were separated and genotyped.A total of 161 alleles were observed in the Russian ethnic minority group,and corresponding allelic frequencies ranged from 0.0044 to 0.5965.The 21 non-CODIS STR loci of the Russian ethnic minority group were characterized by high genetic diversity and therefore may be useful for elucidating the population's genetic background,for individual identification,and for paternity testing in forensic practice.

  5. DNA双链断裂修复与重症联合免疫缺陷%DNA double-strand breaks repair and severe combined immunodeficiencies

    Institute of Scientific and Technical Information of China (English)

    王坤英; 赵艳红; 李卫国


    DNA双链断裂(double-strand breaks, DSBs)是细胞DNA损伤的主要类型,它的修复通过同源重组(HR)和非同源末端连接(NHEJ)两种机制实现.NHEJ是人和哺乳动物细胞DSBs修复的重要通路,主要由DNA依赖性蛋白激酶(DNA-PK)、X射线修复交叉互补蛋白4(XRCC4)、DNA连接酶Ⅳ、Artemis、XLF/Cernunnos和其它DNA损伤修复辅助因子组成.本文重点介绍了NHEJ机制主要成分的特性及其功能,以及这些组分的基因发生突变或缺失所引起的DSBs修复缺陷与辐射敏感性重症联合免疫缺陷(radiosensitive severe combined immunodeficiencies, RS-SCIDs).

  6. Maturation of dendritic cells by recombinant human CD40L-trimer leads to a homogeneous cell population with enhanced surface marker expression and increased cytokine production

    DEFF Research Database (Denmark)

    Würtzen, P A; Nissen, Mogens Holst; Claesson, M H


    Dendritic cells (DC) have been shown to be potent inducers of specific cytotoxic T-cell responses both in vivo and in vitro. Furthermore, exposure to cytokines such as tumour necrosis factor (TNF)-alpha or CD40 triggering changes DC phenotype and cytokine production and may enhance the T...... enhanced by exposure to huCD40LT even compared to TNF-alpha exposure. Only a moderate cytokine production was observed initially, while TNF-alpha addition or CD40 triggering, especially, induced enhanced production of IL-6 and IL-12 p40. Surprisingly, comparable induction of T-cell proliferation by a DC...... marker expression and high production of pro-inflammatory cytokines. In addition, the induction of responses to allo or recall antigens presented by huCD40LT maturated DC was comparable to the responses obtained with the DC maturated through TNF-alpha exposure....

  7. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan


    ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair......ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair...

  8. Identification of human DNA in forensic evidence by loop-mediated isothermal amplification combined with a colorimetric gold nanoparticle hybridization probe. (United States)

    Watthanapanpituck, Khanistha; Kiatpathomchai, Wansika; Chu, Eric; Panvisavas, Nathinee


    A DNA test based on loop-mediated isothermal amplification (LAMP) and colorimetric gold nanoparticle (AuNP) hybridization probe to detect the presence of human DNA in forensic evidence was developed. The LAMP primer set targeted eight regions of the human cytochrome b, and its specificity was verified against the DNA of 11 animal species, which included animals closely related to humans, such as chimpanzee and orangutan. By using the AuNP probe, sequence-specific LAMP product could be detected and the test result could be visualized through the change in color. The limit of detection was demonstrated with reproducibility to be as low as 718 fg of genomic DNA, which is equivalent to approximately 100 plasmid DNA copies containing the cytochrome b DNA target region. A simple DNA extraction method for the commonly found forensic biological samples was also devised to streamline the test process. This LAMP-AuNP human DNA test showed to be a robust, specific, and cost-effective tool for the forensic identification of human specimens without requiring sophisticated laboratory instruments.

  9. Combining pseudo dinucleotide composition with the Z curve method to improve the accuracy of predicting DNA elements: a case study in recombination spots. (United States)

    Dong, Chuan; Yuan, Ya-Zhou; Zhang, Fa-Zhan; Hua, Hong-Li; Ye, Yuan-Nong; Labena, Abraham Alemayehu; Lin, Hao; Chen, Wei; Guo, Feng-Biao


    Pseudo dinucleotide composition (PseDNC) and Z curve showed excellent performance in the classification issues of nucleotide sequences in bioinformatics. Inspired by the principle of Z curve theory, we improved PseDNC to give the phase-specific PseDNC (psPseDNC). In this study, we used the prediction of recombination spots as a case to illustrate the capability of psPseDNC and also PseDNC fused with Z curve theory based on a novel machine learning method named large margin distribution machine (LDM). We verified that combining the two widely used approaches could generate better performance compared to only using PseDNC with a support vector machine based (SVM-based) model. The best Mathew's correlation coefficient (MCC) achieved by our LDM-based model was 0.7037 through the rigorous jackknife test and improved by ∼6.6%, ∼3.2%, and ∼2.4% compared with three previous studies. Similarly, the accuracy was improved by 3.2% compared with our previous iRSpot-PseDNC web server through an independent data test. These results demonstrate that the joint use of PseDNC and Z curve enhances performance and can extract more information from a biological sequence. To facilitate research in this area, we constructed a user-friendly web server for predicting hot/cold spots, HcsPredictor, which can be freely accessed from . In summary, we provided a united algorithm by integrating Z curve with PseDNC. We hope this united algorithm could be extended to other classification issues in DNA elements.

  10. Combining combing and secondary ion mass spectrometry to study DNA on chips using 13C and 15N labeling [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Armelle Cabin-Flaman


    Full Text Available Dynamic secondary ion mass spectrometry (D-SIMS imaging of combed DNA – the combing, imaging by SIMS or CIS method – has been developed previously using a standard NanoSIMS 50 to reveal, on the 50 nm scale, individual DNA fibers labeled with different, non-radioactive isotopes in vivo and to quantify these isotopes. This makes CIS especially suitable for determining the times, places and rates of DNA synthesis as well as the detection of the fine-scale re-arrangements of DNA and of molecules associated with combed DNA fibers. Here, we show how CIS may be extended to 13C-labeling via the detection and quantification of the 13C14N- recombinant ion and the use of the 13C:12C ratio, we discuss how CIS might permit three successive labels, and we suggest ideas that might be explored using CIS.

  11. 基于PSCA的肽-DNA复合疫苗的构建及其免疫学效应的检测%Construction of a PSCA based peptide-DNA combined vaccine and its CTLs killing activity identification

    Institute of Scientific and Technical Information of China (English)

    刘勇; 靳凤烁; 张克勤


    This study is aimed to construct a PSCA based peptide-DNA combined vaccine and identify its CTLs killing activity. PLL-PSCA14-22 was obtained by coupling the positively charged poly-lysine (PLL) with a CTL epitope peptide PSCA 14-22. Then DNA/peptide combined vaccine was formed by the self-assembly of a cationic peptide PLL-PSCA14-22 with a plasmid encoding human full-length PSCA gene through electrostatic interactions. The preparation of this combined vaccine was then identified with both DNA retardation and Dnase I protection experiments. The transfection efficiency and CTLs killing activity were evaluated by RT-PCR and LDH release assay, respectively. The protection of DNA was begun at the charge ratios of peptide/DNA≥2, at which DNA was completely retarded in the DNA retardation assay. The PSCA transcripts was existed in the combined vaccine-transfected Hela cells and CTLs killing activity was induced in vivo, which led to the obvious killing of PSCA-positive LNCaP cells. The PSCA-based peptide-DNA combined vaccine can be transfected into eukaryotic cells and induce specific CTLs response and kill PSCA-positive LNCaP cells effectively, which may pave a way for further studies in animals.%目的 设计、制备和鉴定PLL-PSCA 14-22/-pcDNA3.1 (+)-PSCA复合疫苗及其免疫学效应的检测.方法 将带正电荷的多聚赖氨酸(PLL)通过化学方法与PSCA的一个CTL表位肽PSCA14-22偶联,将上述阳离子多肽PLL-PSCA 14-22与带负电荷的编码PSCA的重组质粒pcDNA3.1 (+)-PSCA利用正负电荷相吸作用制备靶向PSCA的肽-DNA复合疫苗;通过DNA阻滞实验和DNase Ⅰ保护实验鉴定制备的疫苗;将制备成功的复合疫苗体外转染Hela细胞,通过RT-PCR检测该疫苗的转染效率;并进一步通过LDH释放实验检测该疫苗对PSCA阳性的前列腺癌细胞系LNCaP的特异性杀伤效应.结果 当PLL-PSCA 14-22多肽与pcDNA3.1 (+)-PSCA重组质粒正负电荷比≥2时,DNA电泳条带完全消失,即重组质粒pcDNA

  12. Application of cpDNA Marker Technique in Parents Selection and Combination of Potato Breeding%cpDNA标记在马铃薯杂交亲本选配中的应用

    Institute of Scientific and Technical Information of China (English)

    胡祚; 郝大海; 段晓艳; 王兆富; 李周; 苏跃; 冯泽蔚; 李灿辉


    Parents selection and combination is the initiate and important step to potato breeding program. U-sing chloroplast DNA ( cpDNA) marker technique, the author detected cytoplast genetic background of the parents and 380 clones derived from hybrid true potato seeds of two cross combinations (Shepody x CIP 004 n = 187 and PB 06 x CIP 004 n = 193 ) . Results showed that Shepody harbored T-type markers of cpDNA which was subjected to the Tuberosum subspecies of Solarium tuberosum L. , but both PB 06 and CIP 004 had A-type markers of cpDNA which belonged to the Andigena subspecies of Solarium tuberosum L.. All clones tested could also be divided into two groups which separately shared the same cpDNA markers with female parents, and the averaged growth period of each group tended to female parents, respectively. The aboved results demonstrated that there was a great potential for cpDNA marker technique in parents selection and combination of potato breeding program.%亲本选配是马铃薯杂交育种工作的重点和难点.利用叶绿体DNA(cpDNA)标记方法,对两个马铃薯杂交组合(Shepody×CIP 004和PB 06×CIP 004)的亲本、及其杂交实生种子后代群体的细胞质遗传背景进行了分析.结果显示:Shepody拥有T-型cpDNA标记,属于普通栽培亚种(Solanium tuberosum ssp.tuberosum);CIP004和PB06拥有A-型cpDNA标记,均属于安第斯栽培亚种(Solanium tuberosum ssp.andigena);在cpDNA两个标记位点(H1和H2)上,2个杂交组合实生种子后代群体的细胞质遗传背景分别与其母本完全一致,平均生育期分别与其母本接近.上述结果表明,cpDNA标记技术在马铃薯杂交亲本选配和早世代选育中具有重要的应用价值.

  13. A combined approach of DNA probe and RFLP for family and species identification of larval stages of commercially important aquatic species: A study on the surfclam Spisula solidissima

    Digital Repository Service at National Institute of Oceanography (India)

    Achuthankutty, C.T.

    by agarose gel electrophoresis indicating that colorimetric detection with a probe is more sensitive than ethidium bromide in the visualization of DNA. Restriction enzymes BtsUI and Aval having different restriction sites were used in RFLP analysis...

  14. Modeling and time-dependent dynamics of processes of stimulated depolymerization, auto-repairing, degradation and radiation curing of DNA macromolecules and biopolymers at separated and combined actions of ionizing irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Vysotskii, Vladimir I. E-mail:; Pinchuk, Anatoliy O.; Kornilova, Alla A.; Samoylenko, Igor I


    The time-dependent dynamics of the formation, relaxation and auto-repairing of double breaks of DNA macromolecules at the combined radiation action and non-radiation processes of degradation (e.g. by free radicals) were considered. The auto-repairing of DNA double breaks is connected with the peculiarities of long-range interaction of nucleotide charges, atoms and molecules in the intracellular milieu. The properties of intracellular liquid and the characteristics of force interaction between the end-pairs of nucleotides in the area of DNA break in response to radiation are changed. Each kind of radiation is characterized by a certain effectiveness of the double DNA break formation but simultaneously one creates the conditions for their liquidation. On the basis of the analysis and correlation of these processes the time-dependent theory for DNA degradation was created, including hormesis phenomenon, radiation antagonism, the validity of anomaly influence of low and large doses at sharp and chronic radiation and other effects. The qualitative and quantitative correspondences of the theory and experimental results of radiation biology were obtained.

  15. Single and combined effects of deoxynivalenol mycotoxin and a microbial feed additive on lymphocyte DNA damage and oxidative stress in broiler chickens. (United States)

    Awad, Wageha A; Ghareeb, Khaled; Dadak, Agnes; Hess, Michael; Böhm, Josef


    The immune and intestinal epithelial cells are particularly sensitive to the toxic effects of deoxynivalenol (DON). The aim of this experiment was to study the effects of DON and/or a microbial feed additive on the DNA damage of blood lymphocytes and on the level of thiobarbituric acid reactive substance (TBARS) as an indicator of lipid peroxidation and oxidative stress in broilers. A total of forty 1-d-old broiler chicks were randomly assigned to 1 of 4 dietary treatments (10 birds per group) for 5 wk. The dietary treatments were 1) basal diet; 2) basal diet contaminated with 10 mg DON/kg feed; 3) basal diet contaminated with 10 mg DON/kg feed and supplemented with 2.5 kg/ton of feed of Mycofix Select; 4) basal diet supplemented with Mycofix Select (2.5 kg/ton of feed). At the end of the feeding trial, blood were collected for measuring the level of lymphocyte DNA damage of blood and the TBARS level was measured in plasma, heart, kidney, duodenum and jejunum. The dietary exposure of DON caused a significant increase (P = 0.001) of DNA damage in blood lymphocytes (31.99 ± 0.89%) as indicated in the tail of comet assay. Interestingly addition of Mycofix Select to DON contaminated diet decreased (P = 0.001) the DNA damage (19.82 ± 1.75%) induced by DON. In order to clarify the involvement of lipid peroxidation in the DNA damage of DON, TBARS levels was measured. A significant increase (P = 0.001) in the level of TBARS (23 ± 2 nmol/mg) was observed in the jejunal tissue suggesting that the lipid peroxidation might be involved in the DNA damage. The results indicate that DON is cytotoxic and genotoxic to the chicken intestinal and immune cells and the feed additive have potential ability to prevent DNA damage induced by DON.

  16. Nickel(II), copper(II) and zinc(II) metallo-intercalators: structural details of the DNA-binding by a combined experimental and computational investigation. (United States)

    Lauria, Antonino; Bonsignore, Riccardo; Terenzi, Alessio; Spinello, Angelo; Giannici, Francesco; Longo, Alessandro; Almerico, Anna Maria; Barone, Giampaolo


    We present a thorough characterization of the interaction of novel nickel(II) (1), copper(II) (2) and zinc(II) (3) Schiff base complexes with native calf thymus DNA (ct-DNA), in buffered aqueous solution at pH 7.5. UV-vis absorption, circular dichroism (CD) and viscometry titrations provided clear evidence of the intercalative mechanism of the three square-planar metal complexes, allowing us to determine the intrinsic DNA-binding constants (K(b)), equal to 1.3 × 10(7), 2.9 × 10(6), and 6.2 × 10(5) M(-1) for 1, 2 and 3, respectively. Preferential affinity, of one order of magnitude, toward AT compared to GC base pair sequences was detected by UV-vis absorption titrations of 1 with [poly(dG-dC)]2 and [poly(dA-dT)]2. Structural details of the intercalation site of the three metal complexes within [dodeca(dA-dT)]2 were obtained by molecular dynamics (MD) simulations followed by density functional theory/molecular mechanics (DFT/MM) calculations. The calculations revealed that three major intermolecular interactions contribute to the strong affinity between DNA and the three metal complexes: (1) the electrostatic attraction between the two positively charged triethylammoniummethyl groups of the metal complexes and the negatively charged phosphate groups of the DNA backbone; (2) the intercalation of the naphthalene moiety within the four nitrogen bases of the intercalation site; (3) the metal coordination by exocyclic donor atoms of the bases, specifically the carbonyl oxygen and amine nitrogen atoms. Remarkably, the Gibbs formation free energy calculated for the intercalation complexes of 1, 2 and 3 with [dodeca(dA-dT)]2 in the implicit water solution is in agreement with the experimental Gibbs free energy values obtained from the DNA-binding constants as ΔG° = -RT ln(K(b)). In particular, the DNA-binding affinity trend, 1 > 2 > 3, is reproduced. Finally, the first shell coordination distances calculated for the intercalation complex 3/[dodeca(dA-dT)]2 are in

  17. Sensitive and selective amplification of methylated DNA sequences using helper-dependent chain reaction in combination with a methylation-dependent restriction enzymes. (United States)

    Rand, Keith N; Young, Graeme P; Ho, Thu; Molloy, Peter L


    We have developed a novel technique for specific amplification of rare methylated DNA fragments in a high background of unmethylated sequences that avoids the need of bisulphite conversion. The methylation-dependent restriction enzyme GlaI is used to selectively cut methylated DNA. Then targeted fragments are tagged using specially designed 'helper' oligonucleotides that are also used to maintain selection in subsequent amplification cycles in a process called 'helper-dependent chain reaction'. The process uses disabled primers called 'drivers' that can only prime on each cycle if the helpers recognize specific sequences within the target amplicon. In this way, selection for the sequence of interest is maintained throughout the amplification, preventing amplification of unwanted sequences. Here we show how the method can be applied to methylated Septin 9, a promising biomarker for early diagnosis of colorectal cancer. The GlaI digestion and subsequent amplification can all be done in a single tube. A detection sensitivity of 0.1% methylated DNA in a background of unmethylated DNA was achieved, which was similar to the well-established Heavy Methyl method that requires bisulphite-treated DNA.

  18. C_(60)/Cu~(2+)影响质粒DNA构象的复合效应研究%Combined Effect Study of C60/Cu2+ Affecting Plasmid DNA Conformation

    Institute of Scientific and Technical Information of China (English)

    李佳; 林燕; 李准洁; 李正; 梁勇


    碳纳米材料的毒性效应日益受到广泛关注,通过比较研究多种非光催化条件下,富勒烯(C60)/Cu2+共存时对质粒DNA构象影响的复合作用,借以评估碳纳米材料的毒性效应。实验结果显示在非光催化条件下,C60/Cu2+可显著诱导DNA构象从超螺旋DNA转变成开环DNA,并且这种剪切效应随C60和Cu2+浓度的升高而增强;断裂后的DNA片段可重新被T4DNA连接酶连接成环状DNA,这说明C60/Cu2+的剪切位点为磷酸二酯键。另外,多种活性氧捕获剂均不能有效消除C60/Cu2+对DNA的剪切作用,这与Cu2+在DNA裂解中起主要作用相关。上述研究结果表明在非光催化条件下,C60/Cu2+可有效诱导DNA断裂,具有明显的复合效应,其潜在的基因毒性值得关注。%The toxic effects of carbon nanoparticles have been increasingly gaining attention. In this research, the combined effect of C60/Cu2+ on DNA conformation was comparatively studied by altering various reaction conditions, to assess the biological toxicity of carbon nanoparticles. The results showed that without photoexeitation, C60/Cu2+ could significantly induce the conversion of supercoiled DNA into nicked DNA, and this DNA cleavage effect was enhanced as the concentration of Cu2+ and C60 increased. Moreover, the cleaved DNA could be reconnected to circular DNA by T4 DNA ligase, which indicated that the phosphodiester bond was the splicing site of C60/Cu2+. In addition, various ROS savengers could not reduce the DNA cleavage effect of C60/ Cu2+, which was relate to the feature that Cu2+ played a pivotal role in DNA cleavage. Taken to- gether, these results demonstrated that Ca/Cu2+ could significantly induce the DNA cleavage with- out photoexcitation, which exhibited obvious combined effect. Further consideration should be given in assessment of their potential genotoxicity.

  19. Solid-phase based on-chip DNA purification through a valve-free stepwise injection of multiple reagents employing centrifugal force combined with a hydrophobic capillary barrier pressure. (United States)

    Zhang, Hainan; Tran, Hong Hanh; Chung, Bong Hyun; Lee, Nae Yoon


    In this paper, we demonstrate a simple technique for sequentially introducing multiple sample liquids into microchannels driven by centrifugal force combined with a hydrophobic barrier pressure and apply the technique for performing solid-phase based on-chip DNA purification. Three microchannels with varying widths, all equipped with independent sample reservoirs at the inlets, were fabricated on a hydrophobic elastomer, poly(dimethylsiloxane) (PDMS). First, glass beads were packed inside the reaction chamber, and a whole cell containing the DNA extract was introduced into the widest channel by applying centrifugal force for physical adsorption of the DNA onto the glass beads. Next, washing and elution solutions were sequentially introduced into the intermediate and narrowest microchannels, respectively, by gradually increasing the amount of centrifugal force. Through a precise manipulation of the centrifugal force, the DNA adsorbed onto the glass beads was successfully washed and eluted in a continuous manner without the need to introduce each solution manually. A stepwise injection of liquids was successfully demonstrated using multiple ink solutions, the results of which corresponded well with the theoretical analyses. As a practical application, the D1S80 locus of human genomic DNA, which is widely used for forensic purposes, was successfully purified using the microdevice introduced in this study, as demonstrated through successful target amplification. This will pave the way for the construction of a control-free valve system for realizing on-chip DNA purification, which is one of the most labor-intensive and hard-to-miniaturize components, on a greatly simplified and miniaturized platform employing hydrophobic PDMS.

  20. Treatment of brain glioblastoma multiforme with pcDNA3.1-Egr. 1p-p16 combined with gamma knife radiation: An experimental study on nude mice

    Directory of Open Access Journals (Sweden)

    Liu Wenke


    Full Text Available Background: High post-operative recurrence and poor prognosis are likely to be related to the infiltrative growth of the glioblastoma multiforme (GBM. Objectives: The primary objective of this study is to investigate the possible synergistic effect of the combined treatment of gamma knife radio-surgery (GKRS and gene therapy for GBM and secondary objective is to explore the role of GKRS for the temporal and spatial regulation of the gene expression. Materials and Methods: The study performed on 70 nude mice and randomly divided into seven groups. Subcutaneous injection of human GBM tumor cells (T98G was carried out to establish the animal models. Various doses of liposome-mediated pcDNA3.1-Egr. 1p-p16 recombinant plasmid were transfected through intra-tumor injection. GKRS was scheduled following the plasmid transfection. Tumor volumes were measured every 4 days after the treatment. Subcutaneous tumor nodule specimens were collected to analyze the cell apoptosis and p16 gene expression using terminal-deoxynucleoitidyl transferase mediated nick end labeling staining and reverse transcription-polymerase chain reaction. Tumor volumes, levels of cell apoptosis and p16 gene expression were compared between groups. Results: Rates of tumor growth were significantly lower in the pcDNA3.1-Egr. 1p-p16 plasmid + GKRS groups than that in the remaining groups 28 days following the GKRS management. The p16mRNA expression was noted in both of the pcDNA3.1-Egr. 1p-p16 plasmid group and the pcDNA3.1-Egr. 1p-p16 plasmid + GKRS with marginal-dose of 20 Gy group. The level of messenger ribonucleic acid expression was higher in the pcDNA3.1-Egr. 1p-p16 plasmid + GKRS with the marginal-dose of 20 Gy group, with a markedly increased apoptotic and necrotic cells, than that in the pcDNA3.1-Egr. 1p-p16 plasmid group. Conclusions: In animal studies, pcDNA3.1-Egr. 1p-p16 in combination with GKRS is a preferable management option for the GBM to the sole use of GKRS or gene

  1. Flow cytometric measurement of RNA synthesis based on bromouridine labelling and combined with measurement of DNA content or cell surface antigen

    DEFF Research Database (Denmark)

    Jensen, P O; Larsen, J; Larsen, J K


    RNA synthesis can be analysed in nuclei or cells labelled with 5-bromouridine (BrUrd) and stained using cross-reacting anti-bromodeoxyuridine (BrdUrd) antibody. Flow cytometric dual parameter analysis of BrUrd incorporation and DNA content in nuclear suspensions of human blood lymphocytes showed ...... in HL-60 and K-562 cells was measured simultaneous with CD13 expression....

  2. Detection of Cervical Cancer and High Grade Neoplastic Lesions by a Combination of Liquid‐Based Sampling Preparation and DNA Measurements Using Automated Image Cytometry

    Directory of Open Access Journals (Sweden)

    Xiao Rong Sun


    Full Text Available Objective: To establish if measurements of DNA ploidy could be used to assist cytopathologists and cytotechnologists in population based cervical cancer screening programs in countries where manually reading the slides is impossible due to the lack of sufficient skilled cytotechnologists. The goal of such program is to identify only clinically significant lesions, i.e. those where a clinical intervention to remove the lesion is required immediately. Study Design: A total of 9905 women were enrolled in the study. Cervical samples were taken with a cervix brush that was then placed into a fixative solution. The cells were separated from mucus by mechanical and chemical treatment and then deposited onto microscope slides by a cytocentrifuge. Two slides were prepared from each case; one slide was stained by Papanicolaou stain for manual cytology examination, while the other slide was stained by a DNA specific stain. The latter slide was used to determine the relative amount of DNA in the cell nuclei. Results: A total of 876 women were followed by colposcopy examination where biopsies were taken from the visible lesions or from suspicious areas and histopathology diagnosed 459 as normal or benign cases, 325 as CIN1, 36 as CIN2, 25 as CIN3/CIS, and 31 as invasive cancer. Of these 876 cases, manual cytology called 655 normal or ASCUS, 197 as LSIL, 16 cases as HSIL, and 8 as cancer. DNA measurements found 704 cases having no cells with DNA greater than 5c, 98 cases where there were 1 or 2 cells having DNA amount greater than 5c, and 74 cases where there were 3 or more cells having DNA amount greater than 5c. If manual cytology were to be used to refer all cases of HSIL and cancer to colposcopy and biopsy, 23 lesions that had to be removed would have been discovered (2 CIN2, 11 CIN3/CIS, and 10 cancers, for a sensitivity of 25.0±5.2% at specificity of 99.9±0.1%. If DNA assisted cytology were to be used instead, and all cases having 3 or more cells with

  3. Forensic DNA profiling and database. (United States)

    Panneerchelvam, S; Norazmi, M N


    The incredible power of DNA technology as an identification tool had brought a tremendous change in crimnal justice . DNA data base is an information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers. This article discusses the essential steps in compilation of COmbined DNA Index System (CODIS) on validated polymerase chain amplified STRs and their use in crime detection.

  4. Forensic DNA Profiling and Database


    Panneerchelvam, S.; Norazmi, M. N.


    The incredible power of DNA technology as an identification tool had brought a tremendous change in crimnal justice . DNA data base is an information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers. This article discusses the essential steps in compilation of COmbined DNA Index System (CODIS) on validated polymerase chain amplified STRs and their use in crime detection.

  5. Simultaneous RNA-DNA FISH. (United States)

    Lai, Lan-Tian; Meng, Zhenyu; Shao, Fangwei; Zhang, Li-Feng


    A highly useful tool for studying lncRNAs is simultaneous RNA-DNA FISH, which reveals the localization and quantitative information of RNA and DNA in cellular contexts. However, a simple combination of RNA FISH and DNA FISH often generates disappointing results because the fragile RNA signals are often damaged by the harsh conditions used in DNA FISH for denaturing the DNA. Here, we describe a robust and simple RNA-DNA FISH protocol, in which amino-labeled nucleic acid probes are used for RNA FISH. The method is suitable to detect single-RNA molecules simultaneously with DNA.

  6. The variety identification of QUINA in Brazil based on a combined analysis of DNA barcoding-origin-morphology%基于 DNA 条形码-产地-形态分析联用的巴西马钱属植物药 QUINA 基原鉴定研究

    Institute of Scientific and Technical Information of China (English)

    臧艺玫; 顾选; 余春霞; 肖瑶; 赵百孝; 刘春生; 马长华; 韩丽


    目的:通过 DNA 条形码—产地—形态分析联用的方法对巴西马钱属植物药 QUINA进行基原鉴定研究,为这种药材的开发利用提供依据。方法通过提取样品 DNA、PCR 扩增及双向测序,获得样品的内转录间隔区(internal transcribed spacer,ITS)序列,利用 NCBI 数据库中的 BLAST功能计算相似度,对其基原进行 DNA 条形码鉴定;根据其产地信息对 DNA 条形码鉴定结果进行筛选和分析;依据其形态特征验证鉴定结果。结果本次收集的植物类药材 QUINA 来源于马钱科马钱属植物 Strychnos pseudo quina A. St.-Hil.的根皮。结论 DNA 条形码—产地—形态三者联用的方法可弥补单一鉴定方法的不足,能够快速、准确的对未知样品进行基原鉴定。%Objective To study the variety identification of QUINA of Strychnos Linn. with the combined analysis of DNA barcoding-origin-morphology and provide an evidence for the exploitation of this kind of herbal in Brazil. Methods ITS sequences were amplified by PCR from genomic DNA and sequenced. , BLAST( basic local alignment search tool) in NCBI database was used to calculate the similarity of sequences to identify the variety of samples; then the DNA barcoding identification results were screened and analyzed in reference to its origin information; finally, the morphological characteristics of samples was used to verify the accuracy of identification. Results QUINA collected from market in Brazil was the root bark of Strychnos pseudo quina A. St. -Hil. Conclusion The combined analysis of DNA barcoding-origin-morphology could make up for the deficit of onefold identification method. It contributes to identifying the variety of unidentified samples quickly and accurately.

  7. Multi-targeting exploration of new 2-aminothiazolyl quinolones: Synthesis, antimicrobial evaluation, interaction with DNA, combination with topoisomerase IV and penetrability into cells. (United States)

    Cheng, Yu; Avula, Srinivasa Rao; Gao, Wei-Wei; Addla, Dinesh; Tangadanchu, Vijai Kumar Reddy; Zhang, Ling; Lin, Jian-Mei; Zhou, Cheng-He


    A series of new potentially multi-targeting antimicrobial 2-aminothiazolyl quinolones were designed, synthesized and characterized by (1)H NMR, (13)C NMR, IR, MS and HRMS spectra. Bioactive assay manifested that some of the prepared compounds showed moderate to good antibacterial and antifungal activities. Noticeably, compound 10f could effectively inhibit the growth of B. typhi and MRSA with MIC values of 1 and 8 μg/mL, respectively. Experimental results revealed that compound 10f was membrane-active and had the ability to rapidly kill the tested strains and effectively prevent the development of bacterial resistance. Moreover, this compound also exhibited low toxicity against L929 cells. Molecular docking indicated that compound 10f could bind with topoisomerase IV-DNA complexes through hydrogen bonds and hydrophobic interactions. Quantum chemical studies were also performed on 10f to understand the structural features essential for activity. The preliminary mechanism research suggested that compound 10f could intercalate into calf thymus DNA to form a steady supramolecular complex which might block DNA replication to exert the powerful bioactivities.

  8. Recent progress in DNA origami technology. (United States)

    Endo, Masayuki; Sugiyama, Hiroshi


    DNA origami is an emerging technology for designing defined two-dimensional DNA nanostructures. In this review, we focus on and describe several types of DNA origami-related studies, as follows: (1) programmed DNA origami assembly, (2) DNA origami-templated molecular assembly, (3) design and construction of various three-dimensional DNA origami structures, (4) programmed functionalization of DNA origami and combination with top-down nanotechnology, (5) single molecular observation on a designed DNA origami, and (6) DNA nanomachines working on a DNA origami.

  9. Proton-Induced X-ray Emission (PIXE) Analysis and DNA-chain Break study in rat hepatocarcinogenesis: A possible chemopreventive role by combined supplementation of vanadium and beta-carotene



    Abstract Combined effect of vanadium and beta-carotene on rat liver DNA-chain break and Proton induced X-ray emission (PIXE) analysis was studied during a necrogenic dose (200 mg/kg of body weight) of Diethyl Nitrosamine (DENA) induced rat liver carcinogenesis. Morphological and histopathological changes were observed as an end point biomarker. Supplementation of vanadium (0.5 ppm ad libitum) in drinking water and beta-carotene in the basal diet (120 mg/Kg of body weight) were performed four ...

  10. A combined DNA-microsatellite and isozyme analysis of the population structure of the harbour porpoise in Danish waters and west Greenland

    DEFF Research Database (Denmark)

    Andersen, L W; Holm, L E; Siegismund, Hans Redlef;


    One hundred and twenty-four specimens of the harbour porpoise, Phocoena phocoena, occurring in inner Danish waters (IDW), the North Sea and West Greenland were analysed to study subdivision into genetically differentiated subpopulations using PCR-amplified DNA-microsatellites and isozyme markers...... or nonrandom mating. The analysis of the genetical population structure showed that harbour porpoises from West Greenland, the North Sea and IDW were three geographically, genetically differentiated populations even though connected through some degree of gene flow. A tendency for females to be more stationary...... than males was suggested. Furthermore, the population structure suggested a closer relationship between IDW and the North Sea....

  11. A tumor targeted therapy study of PcDNA-sTRAIL combined with 131I-angiostatin on lewis lung garcinoma nude mice%131I-血管抑素联合PcDNA-sTRAIL在荷瘤小鼠模型肿瘤靶向治疗的研究

    Institute of Scientific and Technical Information of China (English)

    张弦; 田琼; 魏龙晓; 周润锁; 徐海峰; 袁梦辉


    Objective :To build PcDNA-sTRAIL eukaryolic expression vector and amplify, purify it. Then observe the joint sntitumor effect of the PcDNA-sTRAIL combined with '" I -AS in Lewis Lung Carcinoma nude mice Methods ■ Through the PCR amplification and directional cloning technology to build PcDN A-sTR AIL eukaryotic express carrier, me '" 1 to mark AS. The mark rate could reach 85 'A and exhibit good in vitro stability. After successfully constructed a tumor-burdened nude mice model, then we got a tumor-burdened mice SPECT imaging. Next, we completed a tumor targeted therapy study of restructuring PcON A-sTRAIL combined with '" I -AS. Result the overage volume of tumor in the PcDNA-sTRAIL and '" I-AS combined treatment group is smaller the other single treated groups. Conclusion ?Thi* research firstly suggested the combined treatment of inhibiting tumor angiogenesis effect, promoting the tumor cell apoptosis effect, and radiation treatment to fight cancer. We expect we could not only take full advantages of the three methods, but also provide powerful experimental evidences for combination treatment of radionuclide and the immune therapy.%目的:构建PcDNA-sTRAIL真核表达载体并进行扩增、纯化,采用131I标记血管抑素(AS)并完成了PcDNA-sTRAIL与131I-AS在荷瘤裸鼠体内的联合抑瘤试验.方法;通过PCR扩增和定向克隆技术成功构建PcDNA-sTRAIL真核表达载体,采用131I标记血管抑素,标记率达85%且体外稳定性好,成功构建了荷瘤裸鼠模型,并进行了荷瘤小鼠联合治疗后SPECT显像和病理结果,完成PcDNA-sTRAIL与131I-AS在荷瘤裸鼠体内的联合抑瘤试验.结果:荷瘤小鼠PcDNA-sTRAIL与131I-AS联合用药治疗期间肿瘤平均体积较其他单独治疗组增长缓慢.结论:本研究将抑制肿瘤血管生成、促肿瘤细胞凋亡和放射性核素的内照射三重作用相结合并用于抗肿瘤治疗,期望不仅能充分发挥三者的优势,又能为核素内照射与免疫

  12. Prolonged and severe thrombocytopenia with pancytopenia induced by radiation-combined temozolomide therapy in a patient with newly diagnosed glioblastoma--analysis of O6-methylguanine-DNA methyltransferase status. (United States)

    Nagane, Motoo; Nozue, Kyoko; Shimizu, Saki; Waha, Andreas; Miyazaki, Hiroshi; Kurita, Hiroki; Homori, Masashi; Fujioka, Yasunori; Shiokawa, Yoshiaki


    We report a case of a 51-year-old woman with newly diagnosed glioblastoma multiforme (GBM) who was treated with surgery followed by the standard concomitant temozolomide (TMZ) and radiotherapy (RT). Although TMZ is generally safe and well-tolerated, she developed a sudden onset of prolonged and severe thrombocytopenia as the most prominent event of pancytopenia during the combined treatment, leading to discontinuation of the combined therapy. Thrombocytopenia lasted for more than 2 months with intensive, intermittent platelet transfusions. A bone marrow aspiration and biopsy performed after recovery of severe suppression still revealed reduced number of megakaryocytes. O(6)-methylguanine-DNA methyltransferase (MGMT) analyses showed methylated MGMT promoter in GBM, but unmethylated promoters in both peripheral blood leukocytes and bone marrow cells. This is the first report suggesting the irrelevance of MGMT status of normal hematopoietic cells to TMZ-induced severe thrombocytopenia and pancytopenia.

  13. Detection of Eleven Pathogenic Bacterium Using DNA Microarray Combined With Multiplex PCR%多重PCR结合基因芯片技术检测11种致病菌方法的建立

    Institute of Scientific and Technical Information of China (English)

    贺晨; 孙鸿燕; 邵丽筠; 刘金华; 张春秀; 刘娅


    Objective To establish a rapid ,accurate detection method for 11 kinds of pathogenic bacteria using DNA microarray combined with multiplex PCR .Methods The special genes of these Bacterium including Shigella, Listeria monocytogenes ,Escherichi-a coli O157, Staphylococcus aureus , Bacillus cereus , Campylobacter jejuni, Proteusbacillus vulgaris , C . perfringens , Vibiro para-haemolyticus ,Salmonella typhi ,Salmonella enteritidis were as target genes for multiplex PCR respectively ,then primers and captured oligonucleotide probes were designed and synthesized .After multiplex PCR system and hybridization reaction were optimized ,the multr-plex PCR products were hybridizes with DNA microarray ,which contained specific probes of eleven pathogenic bacterium .Scanner was used to determinant the types of bacterium .Results The DNA microarray assay can detect 11 kinds of pathogenic bacterium specially .The sensitivity of the DNA may reach 2?0-3 ng .Conclusion To detect 11 kinds of pathogenic bacteria using DNA microarray combined with multiplex PCR is specific ,sensiu've ,practical.%目的 建立一种运用多重PCR方法结合基因芯片技术快速、准确检测11种常见致病菌的方法.方法 筛选志贺氏菌、肠炎沙门氏菌、伤寒沙门氏菌、大肠杆菌O157、副溶血性弧菌、普通变形杆菌、蜡样芽孢杆菌、金黄色葡萄球菌、单核细胞增生李斯特菌、产气荚膜梭菌、空肠弯曲菌的特异基因作为目的 基因.设计相应的引物及探针,进行多重PCR扩增,制备寡核苷酸芯片.将多重PCR扩增产物与带有11种特异探针的基因芯片杂交.用扫描仪扫描,判定细菌种类.结果 该基因芯片可特异性地检测11种致病菌,具有良好的特异性,基因组DNA检测灵敏度可达2×10-3ng.结论 多重PCR结合基因芯片技术检测11种不同致病菌的方法特异性好,灵敏度高,具有较好的实用性.

  14. Isolation and identification of spoilage microorganisms using food-based media combined with rDNA sequencing: ranch dressing as a model food. (United States)

    Waite, Joy G; Jones, Joseph M; Yousef, Ahmed E


    Investigating microbial spoilage of food is hampered by the lack of suitable growth media and protocols to characterize the causative agents. Microbial spoilage of salad dressing is sporadic and relatively unpredictable, thus processors struggle to develop strategies to minimize or prevent spoilage of this product. The objectives of this study were to (i) induce and characterize spoilage events in ranch-style dressing as a model food, and (ii) isolate and identify the causative microorganisms using traditional and food-based media, coupled with rDNA sequence analysis. Ranch dressing (pH 4.4) was prepared and stored at 25 degrees C for 14 d and microbial populations were recovered on MRS agar and ranch dressing agar (RDA), a newly formulated food-based medium. When isolates suspected as the spoilage agents were inoculated into ranch dressing and held at 25 degrees C for 9-10 d, three unique spoilage events were characterized. Using rDNA sequence comparisons, spoilage organisms were identified as Lactobacillus brevis, Pediococcus acidilactici, and Torulaspora delbrueckii. P. acidilactici produced flat-sour spoilage, whereas Lb. brevis resulted in product acidification and moderate gas production. The RDA medium allowed for optimum recovery of the excessive gas-producing spoilage yeast, T. delbrueckii. The isolation and identification strategy utilized in this work should assist in the characterization of spoilage organisms in other food systems.

  15. DNA与结核抗体联合检测对结核性胸膜炎的诊断意义%Significance of combined detection of DNA and tuberculosis antibody in the diagnosis of tuberculous pleurisy

    Institute of Scientific and Technical Information of China (English)

    李玉明; 郭明日; 张立


    目的:探讨DNA和结核抗体(TB-Ab)联合检测在结核性胸膜炎的临床诊断意义。方法分别采用斑点金免疫渗滤法和实时荧光定量PCR法对95例结核性胸腔积液患者及45例非结核性胸腔积液患者进行TB-Ab和结核分枝杆菌DNA检测,并对结果进行分析比较。结果结核性胸膜炎组结核分枝杆菌 DNA 检测阳性率为56.8%,显著高于非结核性胸膜炎组(4.4%),差异具有统计学意义(P<0.05)。结核性胸膜炎组TB-Ab检测阳性率为58.9%,显著高于非结核性胸膜炎组(6.6%),差异具有统计学意义(P<0.05)。两项指标应用结核性胸膜炎组阳性率可提高为78.9%,显著高于涂片镜检以及结核菌培养单项检测阳性率,差异具有统计学意(P<0.01)。结论结核分枝杆菌DNA 与TB-Ab 联合检测可明显提高结核性胸膜炎的阳性检出率,而且快速、简便、易操作。%Objective To disscuss the significance of combined detection of DNA and tuberculosis antibody(TB-Ab)in the diag-nosis of tuberculous pleurisy.Methods Dot immunogold filtration assay and real-time fluorescence PCR method were respectively used to detect TB-Ab and DNA of 95 cases of tuberculous pleural effusion patients(tuberculosis pleurisy group)and 45 cases of pa-tients without tuberculous pleural effusion(non-tuberculous pleurisy group).Results were analyzed and compared.Results The positive rate of Mycobacterium tuberculosis DNA in tuberculosis pleurisy group was 5 6 .8%,which was higher than that of non-tu-berculous pleurisy group(4.4%),with significant difference between them(P<0.05).The positive rate of TB-Ab in tuberculosis pleurisy group was 58.9%,higher than that of non tuberculous pleurisy group (6.6%),and the difference was statistically signifi-cant (P<0.05).Combined application of DNA and TB-Ab,the positive rate of tuberculosis pleurisy group could be increased to 78.9%,significantly higher

  16. DNA media storage

    Institute of Scientific and Technical Information of China (English)

    Christy M.Bogard; Eric C.Rouchka; Benjamin Arazi


    In 1994. University of Southern California computer scientist,Dr.Leonard Adleman solved the Hamiltonian path problem using DNA as a computational mechanism.He proved the principle that DNA computing could be used to solve computationally complex problems.Because of the limitations in discovery time,resource requirements,and sequence mismatches,DNA computing has not yet become a commonly accepted practice.However,advancements are continually being discovered that are evolving the field of DNA computing.Practical applications of DNA are not restricted to computation alone.This research presents a novel approach in which DNA could be used as a means of storing files.Through the use of multiple sequence alignment combined with intelligent heuristics,the most probabilistic file contents can be determined with minimal errors.

  17. DNA Media Storage. (United States)

    Bogard, Christy M; Rouchka, Eric C


    In 1994, University of Southern California computer scientist Dr. Leonard Adelman solved the Hamiltonian Path Problem using DNA as a computational mechanism. He proved the principle that DNA computing could be used to solve computationally complex problems. Because of the limitations in discovery time, resource requirements, and sequence mismatches, DNA computing has not yet become a commonly accepted practice. However, advancements are continually being discovered that are evolving the field of DNA Computing. Practical applications of DNA are not restricted to computation alone. This research presents a novel approach in which DNA could be used as a means of storing files. Through the use of Multiple Sequence Alignment combined with intelligent heuristics, the most probabilistic file contents can be determined with minimal errors.

  18. Analysis of immune system gene expression in small rheumatoid arthritis biopsies using a combination of subtractive hybridization and high-density cDNA arrays. (United States)

    Zanders, E D; Goulden, M G; Kennedy, T C; Kempsell, K E


    Subtractive hybridization of cDNAs generated from synovial RNA which had been isolated from patients with rheumatoid arthritis (RA) or normal controls was used in conjunction with high-density array hybridization to identify genes of immunological interest. The method was designed to detect gene expression in small needle biopsy specimens by means of a prior amplification of nanogram amounts of total RNA to full-length cDNA using PCR. The latter was cut with Rsa I, ligated with adapters, hybridized with unmodified driver cDNA, and subjected to suppression subtraction PCR. Differentially expressed products were cloned into E. coli and picked into 384 well plates. Inserts were obtained by PCR across the multiple cloning site, and the products arrayed at high density on nylon filters. The subtracted cDNAs were also labelled by random priming for use as probes for library screening. The libraries chosen were the subtracted one described above and a set of 45,000 ESTs from the I.M. A.G.E consortium. Clones showing positive hybridization were identified by sequence analysis and homology searching. The results showed that the subtracted hybridization approach could identify many gene fragments expressed at different levels, the most abundant being immunoglobulins and HLA-DR. The expression profile was characteristic of macrophage, B cell and plasma cell infiltration with evidence of interferon induction. In addition, a significant number of sequences without matches in the nucleotide databases were obtained, this demonstrates the utility of the method in finding novel gene fragments for further characterisation as potential members of the immune system. Although RA was studied here, the technology is applicable to any disease process even in cases where amounts of tissue may be limited.

  19. Combination therapy with an anti-IL-1β antibody and GAD65 DNA vaccine can reverse recent-onset diabetes in the RIP-GP mouse model. (United States)

    Pagni, Philippe P; Bresson, Damien; Rodriguez-Calvo, Teresa; Bel Hani, Amira; Manenkova, Yulia; Amirian, Natalie; Blaszczak, Alecia; Faton, Sina; Sachithanantham, Sowbarnika; von Herrath, Matthias G


    Type 1 diabetes is thought to be an autoimmune condition in which self-reactive T cells attack insulin-secreting pancreatic β-cells. As a proinflammatory cytokine produced by β-cells or macrophages, interleukin-1β (IL-1β) represents a potential therapeutic target in diabetes. We reasoned IL-1β blockade could be combined with islet antigen-specific approaches involving GAD of 65 kDa (GAD65)-expressing plasmids, as previously shown in combination therapies (CTs) with anti-CD3. Thus, we investigated whether anti-IL-1β antibody alone or combined with GAD65 vaccine could reverse diabetes development in a virus-induced mouse model. Given alone, anti-IL-1β had no effect on diabetes, while GAD65 plasmid resulted in 33% disease reversal after a 5-week observation. However, CTs cured 53% of animals and prevented worsening of glycemic control in nonprotected individuals for up to 12 weeks. While the GAD65 vaccine arm of the CT was associated with increased forkhead box p3(+) regulatory T-cell frequency in pancreatic lymph nodes, islet infiltration by CD11b(+/high) cells was less frequent upon CT, and its extent correlated with treatment success or failure. Altogether, our CTs provided prolonged improvement of clinical and immunological features. Despite unsuccessful clinical trials using anti-IL-1β monotherapy, these data hold promise for treatment of type 1 diabetic patients with IL-1β blockade combined with antigen-specific vaccines.

  20. Use of vibrational spectroscopy to study protein and DNA structure, hydration, and binding of biomolecules: A combined theoretical and experimental approach

    DEFF Research Database (Denmark)

    Jalkanen, Karl J.; Jürgensen, Vibeke Würtz; Claussen, Anetta


    +disp, RHF, MP2, and DFT methodologies for the modeling studies with the goal of interpreting the experimentally measured vibrational spectra for these molecules to the greatest extent possible and to use this combined approach to understand the structure, function, and electronic properties...

  1. Combining a nanosensor and ELISA for measurement of tyrosyl-dna phosphodiesterase 1 (tdp1) activity and protein amount in cell and tissue extract

    DEFF Research Database (Denmark)

    Jakobsen, Ann-Katrine; Stougaard, Magnus


    performed in the exact same aliquot of cell or tissue extract, the combined assay allows the use of minimal amount of cells or tissue and without additional incubation steps compared to the normal ELISA procedure. Measuring protein amount and activity within the same portion of extract also minimizes...

  2. 基于性状-显微-DNA 条形码联用的巴西牛至属植物药 HORTELA 基原鉴定研究%The variety identification of HORTELA in Brazil based on a combined analysis of macroscopic-mi-croscopic-DNA barcoding

    Institute of Scientific and Technical Information of China (English)

    余春霞; 臧艺玫; 顾选; 吴浩忠; 马长华; 韩丽; 刘春生; 赵百孝


    Objective To study the variety identification of HORTELA of Origanum Linn. in Brazil with a combined analysis of macroscopic-microscopic-DNA barcoding. Methods Macroscopic iden-tification was used to identify the authenticity of samples preliminarily; then the results was verified by mi-croscopic identification; finally, ITS sequences were amplified by PCR and sequenced, and BLAST in NCBI ( basic local alignment search tool) database was used to calculate the similarity of sequences to identify variety of samples. Results The combined analysis of macroscopic-microscopic-DNA barcoding indicated that Hortela collected from market in Brazil is the dried overground part of Origanum elongatum (Bonnet) Emb. & Maire. Conclusion HORTELA may be a multi-source herb ,which originates from the dried overground part of Origanum elongatum(Bonnet) Emb. & Maire and Mentha rotundifolia (Linn. ) Huds.%目的:利用性状—显微—DNA 条形码联用的方法对巴西牛至属植物药 HORTELA 进行基原鉴定研究。方法应用性状鉴定的方法初步对药材进行真伪鉴别;再应用显微鉴定的方法验证性状鉴定结果;最后提取样品 DNA,扩增 ITS 序列,利用 NCBI 数据库中的 BLAST 功能分析相似度,对样品品种进行 DNA 条形码鉴定。结果性状—显微—DNA 条形码综合分析结果表明,该样品为牛至属植物 Origanum elongatum(Bonnet) Emb.& Maire.的干燥地上部分。结论 HORTELA 可能为多基原植物类药材,其来源为牛至属 Origanum elongatum (Bonnet) Emb.& Maire.和薄荷属Mentha rotundifolia (Linn.) Huds.干燥地上部分。

  3. Evaluation of the Combined Effect of 2ME2 and Co on the Inducement of DNA Damage by IUdR in a Spheroid Model of the U87MG Glioblastoma Cancer Cell Line Using Alkaline Comet Assay

    Directory of Open Access Journals (Sweden)

    Ali Neshasteh-Riz


    Full Text Available Objective: In this study, we investigated the combined effect of 2-Methoxyestradiol (2ME2and 60Co on the cytogenetic damage of iododeoxyuridine (IUdR in the spheroid model ofU87MG glioblastoma cancer cell lines by alkaline comet assay.Materials and Methods: U87MG cells were cultured as spheroids with diameters of 350μm. As control, the spheroids of one plate were not treated. Other cultures were pretreatedwith 2ME2 (250 μM for one volume doubling time (1 VDT. After this time, the subsequenttreatments were performed according to the following groups:1. Vehicle (this sample was not treated in the 2nd VDT2. Treated with 2ME2 (250 μM for 1 VDT3. Treated simultaneously with 2ME2 (250 μM and IUdR (1 μM for 1 VDT4. Treated with 2ME2 (250 μM for 1 VDT then irradiated with 60Co (2 Gy5. Treated simultaneously with 2ME2 (250 μM and IUdR (1 μM for 1 VDT then irradiatedwith 60Co (2 GyThen the DNA damage was evaluated using the alkaline comet assay method.Results: The results showed that 2ME2 in combination with gamma irradiation of 60Cosignificantly (p<0.001 increased the DNA damage by IUdR as compared to the controlgroup. Thus the combination of these two agents increased the cytogenetic effects ofIUdR in the spheroid culture model of U87MG glioblastoma cell lines.Conclusion: By inhibiting the HIF-1α protein and preventing the G0 phase arrest, 2ME2causes an increased progression into S phase and increases the IUdR absorption. Thenthe DNA damage in the spheroid cells increases as the uptake of IUdR is increased.These results suggest that the combined use of 2ME2 and 60Co can increase the radiosensitizationeffect of IUdR.

  4. X-linked Hyper IgM (HIGM1 in an African kindred: the first report from South Africa

    Directory of Open Access Journals (Sweden)

    Henderson Howard E


    Full Text Available Abstract Background The objective of this study was to describe the clinical and molecular features of the first South African family with X-linked hyper-IgM syndrome (HIGM1. Methods Diagnoses were based on immunoglobulin results and the absence of CD40 ligand (CD40L expression on activated T-cells. Complete molecular characterisation involved CD40L cDNA sequencing, and genomic DNA analysis by polymerase chain reaction amplification, restriction enzyme digestion and sequencing. A PCR-based diagnostic assay was established for carrier detection and prenatal diagnosis in this family. Results There were originally six children, three males and three females. The eldest boy died after being diagnosed with hypogammaglobulinaemia, before HIGM1 was considered. This disorder was diagnosed in the second eldest boy at the age of 5 years, after failing to detect CD40L expression on his activated T-cells. A deficiency of CD40L was also confirmed in the youngest male at the age of 5 years. Both younger brothers have since died of infections relating to HIGM1. Molecular investigation showed that exon 3 was deleted from the CD40L mRNA of the affected males. Genomic DNA analysis identified a 1.5 kilobase deletion, spanning exon 3 and including extended flanking intronic sequence. Carrier status in the mother was confirmed by RT-PCR of her CD40L mRNA. Genetic analysis of the three female children was deferred because they were below the legal consenting age of 18 years. A PCR-based assay for genomic DNA was established for easy identification of female carriers and affected males in the future. Conclusions This study confirmed the diagnosis of HIGM1 in the first South African family to be investigated and identified a novel mutation in the CD40L gene.

  5. CD40 ligand induced cytotoxicity in carcinoma cells is enhanced by inhibition of metalloproteinase cleavage and delivery via a conditionally-replicating adenovirus

    Directory of Open Access Journals (Sweden)

    Young Lawrence S


    Full Text Available Abstract Background CD40 and its ligand (CD40L play a critical role in co-ordinating immune responses. CD40 is also expressed in lymphoid malignancies and a number of carcinomas. In carcinoma cells the physiological outcome of CD40 ligation depends on the level of receptor engagement with low levels promoting cell survival and high levels inducing cell death. The most profound induction of cell death in carcinoma cells is induced by membrane-bound rather than recombinant soluble CD40L, but like other TNF family ligands, it is cleaved from the membrane by matrix metalloproteinases. Results We have generated a replication-deficient adenovirus expressing a mutant CD40L that is resistant to metalloproteinase cleavage such that ligand expression is retained at the cell membrane. Here we show that the mutated, cleavage-resistant form of CD40L is a more potent inducer of apoptosis than wild-type ligand in CD40-positive carcinoma cell lines. Since transgene expression via replication-deficient adenovirus vectors in vivo is low, we have also engineered a conditionally replicating E1A-CR2 deleted adenovirus to express mutant CD40L, resulting in significant amplification of ligand expression and consequent enhancement of its therapeutic effect. Conclusions Combined with numerous studies demonstrating its immunotherapeutic potential, these data provide a strong rationale for the exploitation of the CD40-CD40L pathway for the treatment of solid tumours.

  6. The variety identification of FARINHA DE LARANJA powder in Brazil based on a combined analysis of microscopic-DNA barcoding-origin%基于显微-DNA 条形码-产地分析联用的巴西柑橘属植物药 FARINHA DE LARANJA(枳壳)基原鉴定研究

    Institute of Scientific and Technical Information of China (English)

    臧艺玫; 马条华; 顾选; 余春霞; 王娟; 韩丽; 吴浩忠; 肖瑶; 赵百孝; 刘春生


    Objective o study the variety identification of a kind of herbal powder of FARINHA DE LARANJA of Citrus L. in Brazil with a combaned analysis of microscope - DNA barcoding - origin. Methods Microscopic identification was used to identify the variety of samples preliminarily; then ITS se-quences were amplified by PCR and sequenced, and BLAST in NCBI database was used to calculate the similarity of sequences to identify variety of samples. , Finally, the DNA barcoding identification results were screened and analyzed according to its geographical origin information. Results The combined analysis of microscopic - DNA barcoding - origin indicated that FARINHA DE LARANJA collected from market in Brazil was the dried fruit powder of Citrus aurantium. Conclusion The identification of Brazil FARINHA DE LARANJA could enrich the alternative resources of Zhiqiao and Zhishi.%目的:利用显微-DNA 条形码-产地分析联用的方法对巴西柑橘属植物药 FARINHA DE LARANJA 粉末进行基原鉴定研究。方法应用显微鉴定的方法对药材粉末的基原进行初步判定;再提取样品 DNA,扩增 ITS 序列,利用 NCBI 数据库中的 BLAST 功能分析相似度,对样品品种进行DNA 条形码鉴定;最后结合产地信息对数据库中的序列进行筛选。结果显微-DNA 条形码-产地综合分析结果表明,该样品为芸香科柑橘属 Citrus L.植物酸橙 Citrus aurantium 的干燥未成熟果实粉末。结论巴西植物药 FARINHA DE LARANJA 的鉴定可为扩大枳实、枳壳等中药材的药用资源提供依据。

  7. Combined low initial DNA damage and high radiation-induced apoptosis confers clinical resistance to long-term toxicity in breast cancer patients treated with high-dose radiotherapy

    Directory of Open Access Journals (Sweden)

    Bordón Elisa


    Full Text Available Abstract Background Either higher levels of initial DNA damage or lower levels of radiation-induced apoptosis in peripheral blood lymphocytes have been associated to increased risk for develop late radiation-induced toxicity. It has been recently published that these two predictive tests are inversely related. The aim of the present study was to investigate the combined role of both tests in relation to clinical radiation-induced toxicity in a set of breast cancer patients treated with high dose hyperfractionated radical radiotherapy. Methods Peripheral blood lymphocytes were taken from 26 consecutive patients with locally advanced breast carcinoma treated with high-dose hyperfractioned radical radiotherapy. Acute and late cutaneous and subcutaneous toxicity was evaluated using the Radiation Therapy Oncology Group morbidity scoring schema. The mean follow-up of survivors (n = 13 was 197.23 months. Radiosensitivity of lymphocytes was quantified as the initial number of DNA double-strand breaks induced per Gy and per DNA unit (200 Mbp. Radiation-induced apoptosis (RIA at 1, 2 and 8 Gy was measured by flow cytometry using annexin V/propidium iodide. Results Mean DSB/Gy/DNA unit obtained was 1.70 ± 0.83 (range 0.63-4.08; median, 1.46. Radiation-induced apoptosis increased with radiation dose (median 12.36, 17.79 and 24.83 for 1, 2, and 8 Gy respectively. We observed that those "expected resistant patients" (DSB values lower than 1.78 DSB/Gy per 200 Mbp and RIA values over 9.58, 14.40 or 24.83 for 1, 2 and 8 Gy respectively were at low risk of suffer severe subcutaneous late toxicity (HR 0.223, 95%CI 0.073-0.678, P = 0.008; HR 0.206, 95%CI 0.063-0.677, P = 0.009; HR 0.239, 95%CI 0.062-0.929, P = 0.039, for RIA at 1, 2 and 8 Gy respectively in multivariate analysis. Conclusions A radiation-resistant profile is proposed, where those patients who presented lower levels of initial DNA damage and higher levels of radiation induced apoptosis were at low

  8. Identification of Differentially Expressed Genes During Anther Abortion of Taigu Genic Male Sterile Wheat by Combining Suppression Subtractive Hybridization and cDNA Array

    Institute of Scientific and Technical Information of China (English)

    Qing-Shan Chang; Rong-Hua Zhou; Xiu-Ying Kong; Zeng-Liang Yu; Ji-Zeng Jia


    Taigu Genic Male Sterile Wheat (TGMSW; Triticum aestivum L.), a dominant genic male sterile germplasm, is of considerable value in the genetic improvement of wheat because of its stable inherence, complete male abortion, and high cross-fertilization rate. To identify specially transcribed genes in sterile anther, a suppression subtractive hybridization (SSH) library was constructed with sterile anther as the tester and fertile anther as the driver. A total of 2 304 SSH inserts amplified by polymerase chain reaction were arrayed using robotic printing. The cDNA arrays were hybridized with 32P-labeled probes prepared from the RNA of forward- and reverse-subtracted anthers. Ninety-six clones were scored as upregulated in sterile anthers compared with the corresponding fertile anthers and some clones were selected for sequencing and analysis in GenBank. Based on their putative functions, 87 non-redundant clones were classified into the following groups: (i) eight genes involved in metabolic processes; (ii) four material transportation genes;(iii) three signal transduction-associated genes; (iv) four stress response and senescence-associated protein genes; (v) seven other functional protein genes; (vi) five genes with no known function; and (vii)another 56 genes with no match to the databases. To test the hybridization efficiency, eight genes were selected and analyzed by Northern blot. The results of the present study provide a comprehensive overview of the genes and gene products involved in anther abortion in TGMSW.

  9. A combined de novo protein sequencing and cDNA library approach to the venomic analysis of Chinese spider Araneus ventricosus. (United States)

    Duan, Zhigui; Cao, Rui; Jiang, Liping; Liang, Songping


    In past years, spider venoms have attracted increasing attention due to their extraordinary chemical and pharmacological diversity. The recently popularized proteomic method highly improved our ability to analyze the proteins in the venom. However, the lack of information about isolated venom proteins sequences dramatically limits the ability to confidently identify venom proteins. In the present paper, the venom from Araneus ventricosus was analyzed using two complementary approaches: 2-DE/Shotgun-LC-MS/MS coupled to MASCOT search and 2-DE/Shotgun-LC-MS/MS coupled to manual de novo sequencing followed by local venom protein database (LVPD) search. The LVPD was constructed with toxin-like protein sequences obtained from the analysis of cDNA library from A. ventricosus venom glands. Our results indicate that a total of 130 toxin-like protein sequences were unambiguously identified by manual de novo sequencing coupled to LVPD search, accounting for 86.67% of all toxin-like proteins in LVPD. Thus manual de novo sequencing coupled to LVPD search was proved an extremely effective approach for the analysis of venom proteins. In addition, the approach displays impeccable advantage in validating mutant positions of isoforms from the same toxin-like family. Intriguingly, methyl esterifcation of glutamic acid was discovered for the first time in animal venom proteins by manual de novo sequencing.

  10. A new method for species identification via protein-coding and non-coding DNA barcodes by combining machine learning with bioinformatic methods.

    Directory of Open Access Journals (Sweden)

    Ai-bing Zhang

    Full Text Available Species identification via DNA barcodes is contributing greatly to current bioinventory efforts. The initial, and widely accepted, proposal was to use the protein-coding cytochrome c oxidase subunit I (COI region as the standard barcode for animals, but recently non-coding internal transcribed spacer (ITS genes have been proposed as candidate barcodes for both animals and plants. However, achieving a robust alignment for non-coding regions can be problematic. Here we propose two new methods (DV-RBF and FJ-RBF to address this issue for species assignment by both coding and non-coding sequences that take advantage of the power of machine learning and bioinformatics. We demonstrate the value of the new methods with four empirical datasets, two representing typical protein-coding COI barcode datasets (neotropical bats and marine fish and two representing non-coding ITS barcodes (rust fungi and brown algae. Using two random sub-sampling approaches, we demonstrate that the new methods significantly outperformed existing Neighbor-joining (NJ and Maximum likelihood (ML methods for both coding and non-coding barcodes when there was complete species coverage in the reference dataset. The new methods also out-performed NJ and ML methods for non-coding sequences in circumstances of potentially incomplete species coverage, although then the NJ and ML methods performed slightly better than the new methods for protein-coding barcodes. A 100% success rate of species identification was achieved with the two new methods for 4,122 bat queries and 5,134 fish queries using COI barcodes, with 95% confidence intervals (CI of 99.75-100%. The new methods also obtained a 96.29% success rate (95%CI: 91.62-98.40% for 484 rust fungi queries and a 98.50% success rate (95%CI: 96.60-99.37% for 1094 brown algae queries, both using ITS barcodes.

  11. Proton-Induced X-ray Emission (PIXE Analysis and DNA-chain Break study in rat hepatocarcinogenesis: A possible chemopreventive role by combined supplementation of vanadium and beta-carotene

    Directory of Open Access Journals (Sweden)

    Kanjilal NB


    Full Text Available Abstract Combined effect of vanadium and beta-carotene on rat liver DNA-chain break and Proton induced X-ray emission (PIXE analysis was studied during a necrogenic dose (200 mg/kg of body weight of Diethyl Nitrosamine (DENA induced rat liver carcinogenesis. Morphological and histopathological changes were observed as an end point biomarker. Supplementation of vanadium (0.5 ppm ad libitum in drinking water and beta-carotene in the basal diet (120 mg/Kg of body weight were performed four weeks before DENA treatment and continued till the end of the experiment (16 weeks. PIXE analysis revealed the restoration of near normal value of zinc, copper, and iron, which were substantially altered when compared to carcinogen treated groups. Supplementation of both vanadium and beta-carotene four weeks before DENA injection was found to offer significant (64.73%, P

  12. Molecular Beacon Enables Combination of Highly Processive and Highly Sensitive Rolling Circle Amplification Readouts for Detection of DNA-Modifying Enzymes

    DEFF Research Database (Denmark)

    Kristoffersen, Emil Laust; Gonzales, Maria; Stougaard, Magnus


    -modifying enzymes like type IB Topoisomerases and subsequently amplified by a rolling circle amplification (RCA) mechanism. The RCA process can be followed in real-time by the addition of a molecular beacon with a fluorophore/quencher pair. Upon hybridization to the amplified product, the fluorophore/quencher pair...... is separated, giving rise to a fluorescent signal, measurable in pseudo real-time using a qPCR machine or in a fluorimeter. The RCA products in complex with the molecular beacon can subsequently be moved to microscopic slides and analyzed in a fluorescence microscope. We describe the proof of the principle...... of this molecular beacon-based method combining the qPCR readout format with the standard Rolling circle Enhanced Enzymatic Assay previously reported. Although the qPCR setup is less sensitive, it allows easy, fast, and high-throughput measurement of enzyme activities. Human Topoisomerase IB (TopIB) is a well...

  13. DNA immunization with fusion of CTLA-4 to hepatitis B virus (HBV core protein enhanced Th2 type responses and cleared HBV with an accelerated kinetic.

    Directory of Open Access Journals (Sweden)

    Ying Yin

    Full Text Available BACKGROUND: Typically, DNA immunization via the intramuscular route induces specific, Th1-dominant immune responses. However, plasmids expressing viral proteins fused to cytotoxic T lymphocyte antigen 4 (CTLA-4 primed Th2-biased responses and were able to induced effective protection against viral challenge in the woodchuck model. Thus, we addressed the question in the mouse model how the Th1/Th2 bias of primed immune responses by a DNA vaccine influences hepatitis B virus (HBV clearance. PRINCIPAL FINDINGS: Plasmids expressing HBV core protein (HBcAg or HBV e antigen and HBcAg fused to the extracellular domain of CTLA-4 (pCTLA-4-HBc, CD27, and full length CD40L were constructed. Immunizations of these DNA plasmids induced HBcAg-specific antibody and cytotoxic T-cell responses in mice, but with different characteristics regarding the titers and subtypes of specific antibodies and intensity of T-cell responses. The plasmid pHBc expressing HBcAg induced an IgG2a-dominant response while immunizations of pCTLA-4-HBc induced a balanced IgG1/IgG2a response. To assess the protective values of the immune responses of different characteristics, mice were pre-immunized with pCTLA-4-HBc and pHBc, and challenged by hydrodynamic injection (HI of pAAV/HBV1.2. HBV surface antigen (HBsAg and DNA in peripheral blood and HBcAg in liver tissue were cleared with significantly accelerated kinetics in both groups. The clearance of HBsAg was completed within 16 days in immunized mice while more than 50% of the control mice are still positive for HBsAg on day 22. Stronger HBcAg-specific T-cell responses were primed by pHBc correlating with a more rapid decline of HBcAg expression in liver tissue, while anti-HBs antibody response developed rapidly in the mice immunized with pCTLA-4-HBc, indicating that the Th1/Th2 bias of vaccine-primed immune responses influences the mode of viral clearance. CONCLUSION: Viral clearance could be efficiently achieved by Th1/Th2-balanced

  14. 血液净化联合DNA免疫吸附治疗重症系统性红斑狼疮的效果%Effect of blood purification combined with DNA immunoadsorption in treatment of severe systemic lupus erythematosus

    Institute of Scientific and Technical Information of China (English)

    鱼强; 刘岐焕; 程范军; 刘晓红; 张有顺


    Objective To analyze and explore the effect and safety of continuous blood purification combined with DNA immunoadsorp-tion,prednisone tablets and cyclophosphamide in the treatment of severe systemic lupus erythematosus. Methods 80 patients with severe systemic lupus erythematosus treated in our hospital were taken as the research objects and were averagely divided into the experimental group and the con-trol group. The control group were treated with DNA immunoadsorption,while the experimental group were treated with continuous blood purifica-tion combined with DNA immunoadsorption. The curative effect,renal function indexes and antinuclear antibody in the two groups were compara-tively analyzed. Results The total effective rate in the experimental group(95. 00℅ )was significantly higher than that in the control group(62. 50℅ )( P ﹤ 0. 05). 2 months of treatment later,the blood urea nitrogen(5. 31 ± 1. 25)mmol/ L and serum creatinine(98. 58 ± 21. 17)μmol/L of the experimental group were significantly better than those of the control group[(7. 23 ± 1. 33)mmol/ L and(128. 38 ± 25. 76)μmol/ L]( P ﹤ 0. 05). ANA(1. 62 ± 0. 41)and anti - ds - DHA antibody(0. 91 ± 0. 42)in the experimental group were significantly higher than those of the control group[(2. 21 ± 0. 69)and(1. 21 ± 0. 62)]( P ﹤ 0. 05). The incidence of adverse reactions in the experimental group(7. 50℅ ) was significantly lower than that in the control group(27. 50℅ )( P ﹤ 0. 05). Antinuclear antibody test group sensitivity of 30. 00℅ was signifi-cantly lower than the 62. 50℅ in the control group,the difference was statistically significant( P ﹤ 0. 05). Conclusion The effect of blood puri-fication combined with DNA immunoadsorption in treatment of severe systemic lupus erythematosus is significant. It can improve the renal function of patients,safe and reliable. It is worthy of promotion.%目的:探讨连续性血液净化联合 DNA 免疫吸附配合泼尼松片、环磷

  15. Close linkage of the locus for X chromosome-linked severe combined immunodeficiency to polymorphic DNA markers in Xq11-q13

    Energy Technology Data Exchange (ETDEWEB)

    de Saint Basile, G.; Arveiler, B.; Oberle, I.; Malcolm, S.; Levinsky, R.J.; Lau, Y.L.; Hofker, M.; Debre, M.; Fischer, A.; Griscelli, C.; Mandel, J.L.


    The gene for X chromosome-linked severe combined immunodeficiency (SCID), a disease characterized by a block in early T-cell differentiation, has been mapped to the region Xq11-q13 by linkage analysis with restriction fragment length polymorphisms. High logarithm of odds (lod) scores were obtained with the marker 19.2 (DXS3) and with the marker cpX73 (DXS159) that showed complete cosegregation with the disease locus in the informative families analyzed. Other significant linkages were obtained with several markers from Xq11 to q22. With the help of a recently developed genetic map of the region, it was possible to perform multipoint linkage analysis, and the most likely genetic order is DXS1-(SCID, DXS159)-DXYS1-DXYS12-DXS3, with a maximum multipoint logarithm of odds score of 11.0. The results demonstrate that the SCID locus (gene symbol IMD4) is not closely linked to the locus of Bruton's agammaglobulinemia (a defect in B-cell maturation). They also provide a way for a better estimation of risk for carrier and antenatal diagnosis.

  16. Toxicity of Combined Exposure to Formaldehyde and Ethylbenzene on DNA Damage in Brain Cells of Mice%甲醛和乙苯联合染毒对小鼠脑组织DNA的损伤

    Institute of Scientific and Technical Information of China (English)

    申梦童; 原福胜


    [Objective] To explore the toxicity of single or combined exposure to formaldehyde and ethylbenzene on DNA damage in brain cells of mice and to analyze the type of joint toxic effect.[Methods] Based on a 4 × 4 factorial experiment design,single cell gel electrophoresis (SCGE) technique was used to investigate DNA damage in mice brain cells exposed to formaldehyde (0,0.2,2.0,and 20.0 mg/kg),ethylbenzene (0,50,250,and 500 mg/kg),and both.[Results] Compared with the control group,the comet cells ratio,the percentage of tail DNA,and the Olive tail moment in all exposure groups increased significantly (P < 0.05).The comet cells ratio showed a significant upward tendency with increasing chemicals' doses,and was significantly elevated in the group treated with high-dose mixture compared with the other exposure groups (P<0.05).The percentage of tail DNA and the Olive tail moment were also increased as the dose of ethylbenzene or formaldehyde increased,but not in the group treated with high dose of formaldehyde.An interaction between toxic effects of formaldehyde and ethylbenzene was identified (P< 0.05).[Gondusion] Formaldehyde and ethlybenzene could cause DNA damage in mice brain cells and the joint exposure show severer effect than either single exposure.The joint toxic effect on DNA damage appears to be synergistic.%[目的]探讨不同浓度甲醛和乙苯单独及联合染毒对小鼠脑组织DNA的损伤作用,分析其联合作用的类型.[方法]采用4×4析因设计,利用单细胞凝胶电泳实验方法,研究甲醛(0、0.2、2.0、20.0 mg/kg)和乙苯(0、50、250、500 mg/kg)单独以及二者联合染毒后小鼠脑组织DNA的损伤情况. [结果]甲醛和乙苯单独及联合染毒组小鼠脑细胞彗星拖尾率、尾部DNA含量和尾矩均高于对照组(P<0.05);彗星细胞拖尾率随染毒剂量的增加而增大,高剂量联合组小鼠的拖尾率高于其他各组(P<0.05);尾部DNA含量和尾矩均随乙苯剂量的增加而增

  17. 宫颈液基细胞学与HPV-DNA在妇科普查中的作用%TCT and the combination of HPV-DNA in the census of women's diseases

    Institute of Scientific and Technical Information of China (English)

    罗业红; 沈琳菲; 邓廷坤; 刘莉


    Objective: to evaluate combine of the liquid-based cytology test and HPV-DNA test in checking gynecological diseases. Methods: This paper has selected 500 samples in all of the gynecological diseases tests form April 2009 to July 2012 randomly to Comparing the detection sensitivity and positive coincidence rate about liquid-based cytology test and HPV-DNA test. This paper adopts TBS grading criteria to comparing the results. The patients who cytological examination result were above ASCUS and HPV positive performed biopsy. Results: Cervical liquid-based cytology diagnostic results show:Normal range and benign reactive cell changing 407 cases (81.4%), HPV - DNA positive cytology diagnosis 106 cases (21.2%), and the pathological diagnosis positive cell 81 cases (16.2%). They are 54 cases confirmed for CIN-I、19 cases for CINII - III and 9 cases for SCC by biopsy. The result show it have huge difference between combine the liquid-based cytology test and HPV-DNA test and any method used alone. The samples are statistically significant (p<0.05).Conclusion: The application of TCT test combine with Higher-risk HPV test and TBS diagnostic criteria can improve the detection rate of cervical lesions.%目的评价液基细胞学检测和HPV-DNA检测的联合应用在妇女病普查中的作用.方法选取2009年4月-2012年07月在我院进行妇女病普查随机抽查的500例当成本文的研究对象,比较液基细胞学检测和HPV检测两种方法的检出敏感性及阳性符合率.诊断应用TBS分级标准,并对细胞学检查诊断为ASCUS以上者和HPV阳性者活检.结果宫颈液基细胞学诊断结果正常范围及良性反应性细胞改变407例(占81.4%),HPV-DNA阳性细胞学诊断106例(占21.2%),病理诊断结果阳性细胞81例(16.2%);经活检证实有54例为CIN-I,CINI-I I 19例,SCC 9例.单用TCT或HPV-DNA检测结果与联合检测比较差异显著,且具有统计学意义(P<0.05).结论 TCT检测结合高危型HPV检测技术的应

  18. Combining Push Pull Tracer Tests and Microbial DNA and mRNA Analysis to Assess In-Situ Groundwater Nitrate Transformations (United States)

    Henson, W.; Graham, W. D.; Huang, L.; Ogram, A.


    Nitrogen transformation mechanisms in the Upper Floridan Aquifer (UFA) are still poorly understood because of karst aquifer complexity and spatiotemporal variability in nitrate and carbon loading. Transformation rates have not been directly measured in the aquifer. This study quantifies nitrate-nitrogen transformation potential in the UFA using single well push-pull tracer injection (PPT) experiments combined with microbial characterization of extracted water via qPCR and RT-qPCR of selected nitrate reduction genes. Tracer tests with chloride and nitrate ± carbon were executed in two wells representing anoxic and oxic geochemical end members in a spring groundwater contributing area. A significant increase in number of microbes with carbon addition suggests stimulated growth. Increases in the activities of denitrification genes (nirK and nirS) as measured by RT-qPCR were not observed. However, only microbes suspended in the tracer were obtained, ignoring effects of aquifer material biofilms. Increases in nrfA mRNA and ammonia concentrations were observed, supporting Dissimilatory Reduction of Nitrate to Ammonia (DNRA) as a reduction mechanism. In the oxic aquifer, zero order nitrate loss rates ranged from 32 to 89 nmol /L*hr with no added carbon and 90 to 240 nmol /L*hr with carbon. In the anoxic aquifer, rates ranged from 18 to 95 nmol /L*hr with no added carbon and 34 to 207 nmol /L*hr with carbon. These loss rates are low; 13 orders of magnitude less than the loads applied in the contributing area each year, however they do indicate that losses can occur in oxic and anoxic aquifers with and without carbon. These rates may include, ammonia adsorption, uptake, or denitrification in aquifer material biofilms. Rates with and without carbon addition for both aquifers were similar, suggesting aquifer redox state and carbon availability alone are insufficient to predict response to nutrient additions without characterization of microbial response. Surprisingly, these

  19. DNA Nanotechnology (United States)

    Taniguchi, Masateru; Kawai, Tomoji


    DNA is one candidate of promising molecules for molecular electronic devices, since it has the double helix structure with pi-electron bases for electron transport, the address at 0.4 nm intervals, and the self-assembly. Electrical conductivity and nanostructure of DNA and modified DNA molecules are investigated in order to research the application of DNA in nanoelectronic devices. It has been revealed that DNA is a wide-gap semiconductor in the absence of doping. The conductivity of DNA has been controlled by chemical doping, electric field doping, and photo-doping. It has found that Poly(dG)[middle dot]Poly(dC) has the best conductivity and can function as a conducting nanowire. The pattern of DNA network is controlled by changing the concentration of the DNA solution.

  20. DNA Methylation


    Alokail, Majed S.; Alenad, Amal M.


    The DNA of E. coli contains 19,120 6-methyladenines and 12,045 5-methylcytosines in addition to the four regular bases and these are formed by the postreplicative action of three DNA methyltransferases. The majority of the methylated bases are formed by the Dam and Dcm methyltransferases encoded by the dam (DNA adenine methyltransferase) and dcm (DNA cytosine methyltransferase) genes. Although not essential, Dam methylation is important for strand discrimination during repair of replication e...

  1. Investigation of Combined Detection of Fecal Occult Blood Test and Fecal DNA Test in the Opportunity Screening for Colorectal Cancer%联合检测粪隐血试验与粪便 DNA 在大肠癌机会性筛查中的探讨

    Institute of Scientific and Technical Information of China (English)

    钟选芳; 甘爱华; 张晓慧; 许岸高; 肖丹


    Objective To investigate the application and significance of opportunistic screening for colorectal cancer using combined detection of fecal occult blood test and fecal DNA test. Methods Forty-six patients with colorectal cancer and 30 normal volunteers were given with opportunistic screening,and were tested using immuno-chemical fecal occult blood tests(IFOBT),as well as the APC,P53 and K-ras mutations in the feces were detected by using polymerase chain reaction single strand conformation polymorphism(PCR-SSCP). Results The positive rate of IFOBT was 45. 7%(21 / 46)and 13. 3%(4 / 30)in the colorectal cancer group and the normal group,respec-tively. Meanwhile,the mutation rate of APC,P53,K-ras genes in the colorectal cancer group were 58. 7%(27 / 46), 65. 2%(30 / 46)and 60. 9%(28 / 46);and were 3. 3%(1 / 30),0. 0%(0 / 30)and 0. 0%(0 / 30)in the normal group. There was no significant difference in the sensitivity and specificity between IFOBT and fecal DNA screening of colorectal cancer,and the sensitivity of joint detection was higher than any single detection method. Conclusion The combined detection of fecal occult blood test and fecal DNA can raise the efficacy of the colorectal cancer screening,it can be used to become an effective noninvasive method of colorectal cancer in the opportunistic screen-ing of early diagnosis and screening.%目的:探讨联合检测粪隐血试验与粪便 DNA 用于大肠癌机会性筛查的应用和意义。方法入组行机会性筛查的46例大肠癌患者和30例正常者的粪便,分别应用免疫法粪便隐血试验(IFOBT)2次,应用PCR-SSCP 方法检测粪便中 APC、P53和 K-ras 基因突变情况。结果大肠癌组和正常组粪便 IFOBT 的阳性率分别为45.7%(21/46)和13.3%(4/30),APC、P53、K-ras 的突变率分别为58.7%(27/46)、65.2%(30/46)、60.9%(28/46)和3.3%(1/30)、0.0%(0/30)、0.0%(0/30),IFOBT 和粪便 DNA 筛查大肠癌的敏感性和特异性差

  2. Isolation, cDNA sequence analysis and tissue expression profile of a novel swine gene differentially expressed in the Longissimus dorsi muscle tissues from Large White × Meishan cross combination

    Institute of Scientific and Technical Information of China (English)

    LIU Yonggang; LEI Minggang; XIONG Yuanzhu; DENG Changyan


    In order to study the molecular mechanism of heterosis in pigs, the mRNA differential display technique was performed to investigate the differences in gene expression in the Longissimus dorsi muscle tissues from Large White × Meishan cross combination.One novel gene differentially expressed between the hybrids and the purebreds was isolated and subsequently identified using semi-quantitative reverse transcriptase polymerase chain reaction (RT-PCR) and its complete cDNA sequence was obtained using the rapid amplification of cDNA ends (RACE) method. The nucleotide sequence of the gene is not homologous to any of the known porcine genes. The sequence prediction revealed that the open reading frame of this gene encodes a protein of 188 amino acids that contains the putative conserved domain of the PRA1 family protein and this protein has high homology with the PRA1 family protein 3 of three species-rat (88 % ), human(88 % ), and mouse (87 % ), -so that it can be defined as swine PRA1 family protein 3. The phylogenetic tree analysis revealed that the swine PRA1 family protein 3 has a closer genetic relationship with the human PRA1 family protein 3 than with those of mouse and rat.The tissue expression analysis indicated that swine PRA1family protein 3 gene is highly-expressed in muscle and fat, moderately in spleen,weakly in heart, kidney, ovary, lung, and almost not expressed in small intestine and liver. The function of this gene and the relationship between this gene and heterosis are also discussed.

  3. Effect of adefovir dipivoxil combined therapy with lamivudine on renal cell mitochondrial DNA in rats%阿德福韦酯联合拉米夫定对大鼠肾细胞线粒体DNA的影响

    Institute of Scientific and Technical Information of China (English)

    王司; 朱新宇


    目的:探讨ADV和LAM联合应用对大鼠肾细胞线粒体DNA的损伤情况。方法 SD大鼠随机分为LAM组、ADV组、ADV + LAM组和空白对照组,连续灌胃给药8周后,采用实时荧光定量PCR (real-time PCR)法检测各组大鼠肾细胞线粒体细胞色素b的基因含量;同时检测各组大鼠的血肌酐、尿素氮水平。并对数据进行单因素方差分析。结果 LAM组、ADV组、ADV + LAM组大鼠肾细胞线粒体细胞色素b的基因含量分别为0.79±0.12、0.59±0.13、0.42±0.89,较空白对照组(1.00±0.00)明显减少(F =63.72,P =0.00);其中ADV组较LAM组基因含量低,t =3.48,P <0.01;ADV + LAM组与LAM组、ADV组两个单药组相比,基因含量最低(t =7.66、3.51,P均<0.01)。而各组大鼠血肌酐、尿素氮水平差异均无统计学意义(P =0.14、0.08)。结论连续给药8周,LAM组、ADV组、ADV + LAM组的肾细胞线粒体DNA水平均有所下降,其中ADV + LAM组线粒体DNA含量下降最明显,即两药联用组的线粒体DNA损伤最重。%Objective To explore the damage of mitochondrial DNA of the kindey induced by lamivudine (LAM) and adefovir dipivoxil (ADV) combined therapy in rats. Methods Forty healthy Sprague-Dawley rats were randomly divided into four equal groups and treated by oral gavage with ADV [40 mg/(kg·d)], LAM [300 mg/(kg·d)], ADV [40 mg/(kg·d)] + LAM [300 mg/(kg·d)], or saline (equal volume) for 8 weeks. DNA of the kindey was purified from each sample and the mitochondrial DNA (mtDNA) content of the kindey was monitored by quantitative real time PCR. At the same time, the levels of serum creatinine and urea nitrogen were deteced. One-way ANOVA, the LSD t-test and Dunnett’s T3 were used for data. Results Compared with blank control group, the mtDNA content of rats treated with LAM group, ADV group and ADV + LAM group significantly decreased (1.00 ± 0.00, F = 63.72, P < 0.01), which were 0.79 ± 0.12, 0

  4. Dna Sequencing (United States)

    Tabor, Stanley; Richardson, Charles C.


    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  5. Biosensors for DNA sequence detection (United States)

    Vercoutere, Wenonah; Akeson, Mark


    DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

  6. Premeltons in DNA. (United States)

    Sobell, Henry M


    Premeltons are examples of emergent-structures (i.e., structural-solitons) that arise spontaneously in DNA due to the presence of nonlinear-excitations in its structure. They are of two kinds: B-B (or A-A) premeltons form at specific DNA-regions to nucleate site-specific DNA melting. These are stationary and, being globally-nontopological, undergo breather-motions that allow drugs and dyes to intercalate into DNA. B-A (or A-B) premeltons, on the other hand, are mobile, and being globally-topological, act as phase-boundaries transforming B- into A-DNA during the structural phase-transition. They are not expected to undergo breather motions. A key feature of both types of premeltons is the presence of an intermediate structural-form in their central regions (proposed as being a transition-state intermediate in DNA-melting and in the B- to A-transition), which differs from either A- or B-DNA. Called beta-DNA, this is both metastable and hyperflexible--and contains an alternating sugar-puckering pattern along the polymer backbone combined with the partial unstacking (in its lower energy-forms) of every-other base-pair. Beta-DNA is connected to either B- or to A-DNA on either side by boundaries possessing a gradation of nonlinear structural-change, these being called the kink and the antikink regions. The presence of premeltons in DNA leads to a unifying theory to understand much of DNA physical chemistry and molecular biology. In particular, premeltons are predicted to define the 5' and 3' ends of genes in naked-DNA and DNA in active-chromatin, this having important implications for understanding physical aspects of the initiation, elongation and termination of RNA-synthesis during transcription. For these and other reasons, the model will be of broader interest to the general-audience working in these areas. The model explains a wide variety of data, and carries with it a number of experimental predictions--all readily testable--as will be described in this review.

  7. DNA-templated nanofabrication. (United States)

    Becerril, Héctor A; Woolley, Adam T


    Nanofabrication, or the organizational control over matter at the nanometre scale, is an intriguing scientific challenge requiring multidisciplinary tools for its solution. DNA is a biomolecule that can be combined with other nanometre-scale entities through chemical self-assembly to form a broad variety of nanomaterials. In this tutorial review we present the principles that allow DNA to interact with other chemical species, and describe the challenges and potential applications of DNA as a template for making both biological and inorganic features with nanometre resolution. As such, this report should be of interest to chemists, surface and materials scientists, biologists, and nanotechnologists, as well as others who seek to use DNA in nanofabrication.

  8. Ridgelet neural network model for short-term wind power forecasting based on the combination of chaos DNA genetic and particle swarm optimization algorithm%基于混沌 DNA 遗传算法与 PSO 组合优化的RNN 短期风电功率预测

    Institute of Scientific and Technical Information of China (English)

    周洪煜; 曾济贫; 王照阳; 赵乾


    Increasing the prediction accuracy of short-term wind power plays a key role in improving the security and stability of electric grid system. Aiming at the characteristics of wind speed signal, this paper uses the Ridgelet Neural Network for building the short-term wind power forecasting model. At the same time we use the chaos DNA genetic to identify the hidden layer of Ridgelet Neural Network, and use the Particle Swarm Optimization algorithm to adjust the weight value and direction vector. Based on the measured historical data of wind farm in Xinjiang, we did a experiment on wind power forecasting and compared the performance of the optimized model with that of the original one. Experimental results indicate that the RMSE(root mean squared error)of Ridgelet Neural Network can reduce to 12. 3% by using the combination of chaos DNA genetic and particle swarm optimization algorithm, and the prediction accuracy is improved significantly.%  提高短期风电功率的预测精度对保证电力系统安全、稳定地运行具有重大意义.针对风速信号的强奇异性,采用脊波神经网络建立短期风电功率的预测模型;同时利用混沌 DNA 遗传算法确定脊波神经网络的隐层结构,采用粒子群算法优化网络的连接权值及方向向量.对新疆某风电场的输出功率进行了预测实验,并比较了优化前后脊波网络模型的预测性能.研究结果表明采用粒子群与混沌 DNA 遗传算法组合优化后的脊波神经网络均方根误差降至12.3%,预测精度得到显著提高.

  9. Effects of oxaliplatin on DNA condensation

    Institute of Scientific and Technical Information of China (English)

    JU HaiPeng; ZHANG HongYan; LI Wei; WANG PengYe


    In this paper the interactions between DNA and anti-cancer drug oxaliplatin were investigated by using magnetic tweezers.The dynamics of DNA condensation due to oxaliplatin was traced under various forces.It is found that torsion constraint in DNA enhances the ability of oxaliplatin for shortening DNA.The transplatin helps oxaliplatin combine to DNA and increase the rate of DNA condensation.All these results are consistent to the previously proposed model and are helpful for further investigation of interaction between DNA and oxaliplatin.

  10. Random amplified polymorphic DNA combined with microfluidic chips in the identification of Malassezia species%随机扩增多态性DNA结合微流芯片鉴定马拉色菌的初步研究

    Institute of Scientific and Technical Information of China (English)

    王韵茹; 章强强


    stable and clear amplification bands than that with S24.Positive bands of different sizes were repetitively obtained by using microfluidic chips,with interspecies and intraspecies polymorphisms observed in all the strains.On the basis of DNA sequencing,microfluidic chips and RAPD-PCR could be used to successfully distinguish the following eight species,i.e.,M.furfur,M.sympodialis,M.globosa,M.pacbydermatis,M.slooffiae,M.Japonica,M.yamatoensis and M.dermatis.Conclusions As a rapid,high-throughput and high-sensitivity method,microfluidic chips combined with RAPD-PCR shows an advantage for analyzing interspecies genetic diversity,genetic relationship of Malassezia species,as well as for identifying new Malassezia species.

  11. Individual and Combined Expression of DNA Damage Response Molecules PARP1, γH2AX, BRCA1, and BRCA2 Predict Shorter Survival of Soft Tissue Sarcoma Patients (United States)

    Park, See-Hyoung; Park, Hye Jeong; Wang, Sung Il; Park, Ho Sung; Lee, Ho; Kwon, Keun Sang; Moon, Woo Sung; Lee, Dong Geun; Kim, Jung Ryul; Jang, Kyu Yun


    DNA damage response (DDR) molecules are protective against genotoxic stresses. DDR molecules are also involved in the survival of cancer cells in patients undergoing anti-cancer therapies. Therefore, DDR molecules are potential markers of cancer progression in addition to being potential therapeutic targets. In this study, we evaluated the immunohistochemical expression of PARP1, γH2AX, BRCA1, and BRCA2 and their prognostic significance in 112 cases of soft tissue sarcoma (STS). The expression of PARP1, γH2AX, BRCA1, and BRCA2 were significantly associated with each other and were associated with higher tumor stage and presence of distant metastasis. The expression of PARP1, γH2AX, and BRCA2 were significantly associated with shorter disease-specific survival (DSS) and event-free survival (EFS) by univariate analysis. BRCA1 expression was associated with shorter DSS. Multivariate analysis revealed the expression of PARP1 and γH2AX to be independent indicators of poor prognosis of DSS and EFS. BRCA2 expression was an independent indicator of poor prognosis of DSS. In addition, the combined expressional patterns of PARP1, γH2AX, BRCA1, and BRCA2 (CSddrm) were independent prognostic predictors of DSS (P DSS rate of the CSddrm-low, CSddrm-intermediate, and CSddrm-high subgroups were 81%, 26%, and 0%, respectively. In conclusion, this study demonstrates that the individual and combined expression patterns of the DDR molecules PARP1, γH2AX, BRCA1, and BRCA2 could be predictive of the prognosis of STS patients and suggests that controlling the activity of these DDR molecules could be employed in new therapeutic stratagems for the treatment of STS. PMID:27643881

  12. Detection of DNA virus in respiratory samples of children by multiplex PCR combined with RDB%PCR-RDB技术快速检测儿童急性呼吸道感染DNA病毒的研究

    Institute of Scientific and Technical Information of China (English)

    田海清; 曾跃红; 王新华; 周勇军


    Objective To develop multiplex polymerase chain reaction (PCR) combined with reversedotblothy bridization (RDB) method for detection of DNA virus in respiratory samples,and provide a surveillance and rapid diagnosis tool of acute viral respiratory infection.Methods We designed multiple PCR primers and the probes referenced to virus nucleic acid sequences in the National Center for Biotechnology Information (NCBI) database,and fixed specific oligonucleotide probes on the nylon membrane.After multiple PCR amplification of virus DNA of human bocavirus (hBOV),karolinska Institutet (KI),adenovirus (AdV),Washington University polyomaviros (WUPyV),and human parvovirus B19 (HPVBI9),the denaturalized amplification products were hybridized with various specific probes,followed by visualization and analysis of the results.The sensitivity and specificity were tested.At the same time,108 cases of clinical specimens of multiple PCR products were analyzed by reverse spot hybridization detection,and compared to the results of culture method.Results The specific probes of multiple PCR-RDB only hybridized with corresponding amplification products without cross-hybridization reaction with other pathogen.The sensitivity of RDB hybridization was 1 colony-forming units (CFU).The positive rate of 34.26% (37 cases out of 108 cases) with PCR-RDB method was significandy higher than that 27.78% (30 cases out of 108 cases) with common test method.Conclusions The multiplex PCR combined with RDB might become a rapid and simple method to detect the DNA virus in respiratory samples,which might be a promising tool for clinical application.%目的 建立多重PCR反向斑点杂交方法(PCR-RDB)技术快速检测儿童急性呼吸道感染DNA病毒,以便及时监测并快速诊断急性病毒性呼吸道感染.方法 参照国家生物技术信息中心(NCBI)数据库病毒核酸序列设计多重PCR引物和探针,将特异的寡核苷酸探针固定于尼龙膜上.利用多重PCR对人博

  13. DNA-PK assay (United States)

    Anderson, Carl W.; Connelly, Margery A.


    The present invention provides a method for detecting DNA-activated protein kinase (DNA-PK) activity in a biological sample. The method includes contacting a biological sample with a detectably-labeled phosphate donor and a synthetic peptide substrate defined by the following features to provide specific recognition and phosphorylation by DNA-PK: (1) a phosphate-accepting amino acid pair which may include serine-glutamine (Ser-Gln) (SQ), threonine-glutamine (Thr-Gln) (TQ), glutamine-serine (Gln-Ser) (QS), or glutamine-threonine (Gln-Thr) (QT); (2) enhancer amino acids which may include glutamic acid or glutamine immediately adjacent at the amino- or carboxyl- side of the amino acid pair and forming an amino acid pair-enhancer unit; (3) a first spacer sequence at the amino terminus of the amino acid pair-enhancer unit; (4) a second spacer sequence at the carboxyl terminus of the amino acid pair-enhancer unit, which spacer sequences may include any combination of amino acids that does not provide a phosphorylation site consensus sequence motif; and, (5) a tag moiety, which may be an amino acid sequence or another chemical entity that permits separating the synthetic peptide from the phosphate donor. A compostion and a kit for the detection of DNA-PK activity are also provided. Methods for detecting DNA, protein phosphatases and substances that alter the activity of DNA-PK are also provided. The present invention also provides a method of monitoring protein kinase and DNA-PK activity in living cells. -A composition and a kit for monitoring protein kinase activity in vitro and a composition and a kit for monitoring DNA-PK activities in living cells are also provided. A method for identifying agents that alter protein kinase activity in vitro and a method for identifying agents that alter DNA-PK activity in living cells are also provided.

  14. Radiation response and regulation of apoptosis induced by a combination of TRAIL and CHX in cells lacking mitochondrial DNA: A role for NF-{kappa}B-STAT3-directed gene expression

    Energy Technology Data Exchange (ETDEWEB)

    Ivanov, Vladimir N., E-mail:; Ghandhi, Shanaz A.; Zhou, Hongning; Huang, Sarah X.; Chai, Yunfei; Amundson, Sally A.; Hei, Tom K.


    Mitochondrial DNA depleted ({rho}{sup 0}) human skin fibroblasts (HSF) with suppressed oxidative phosphorylation were characterized by significant changes in the expression of 2100 nuclear genes, encoding numerous protein classes, in NF-{kappa}B and STAT3 signaling pathways, and by decreased activity of mitochondrial death pathway, compared to the parental {rho}{sup +} HSF. In contrast, the extrinsic TRAIL/TRAIL-Receptor mediated death pathway remained highly active, and exogenous TRAIL in a combination with cycloheximide (CHX) induced higher levels of apoptosis in {rho}{sup 0} cells compared to {rho}{sup +} HSF. Global gene expression analysis using microarray and qRT-PCR demonstrated that mRNA expression levels of many growth factors and their adaptor proteins (FGF13, HGF, IGFBP4, IGFBP6, and IGFL2), cytokines (IL6, {Oota}L17{Beta}, {Oota}L18, {Oota}L19, and {Oota}L28{Beta}) and cytokine receptors (IL1R1, IL21R, and IL31RA) were substantially decreased after mitochondrial DNA depletion. Some of these genes were targets of NF-{kappa}B and STAT3, and their protein products could regulate the STAT3 signaling pathway. Alpha-irradiation further induced expression of several NF-{kappa}B/STAT3 target genes, including IL1A, IL1B, IL6, PTGS2/COX2 and MMP12, in {rho}{sup +} HSF, but this response was substantially decreased in {rho}{sup 0} HSF. Suppression of the IKK-NF-{kappa}B pathway by the small molecular inhibitor BMS-345541 and of the JAK2-STAT3 pathway by AG490 dramatically increased TRAIL-induced apoptosis in the control and irradiated {rho}{sup +} HSF. Inhibitory antibodies against IL6, the main activator of JAK2-STAT3 pathway, added into the cell media, also increased TRAIL-induced apoptosis in HSF, especially after alpha-irradiation. Collectively, our results indicated that NF-{kappa}B activation was partially lost in {rho}{sup 0} HSF resulting in downregulation of the basal or radiation-induced expression of numerous NF-{kappa}B targets, further suppressing IL6

  15. Evaluation of combined high-efficiency DNA extraction and real-time PCR for detection of Mycobacterium avium subsp. paratuberculosis in subclinically infected dairy cattle: comparison with faecal culture, milk real-time PCR and milk ELISA

    Directory of Open Access Journals (Sweden)

    Logar Katarina


    Full Text Available Abstract Background Johne’s disease is caused by Mycobacterium avium subsp. paratuberculosis (Map and it is one of the most important diseases in cattle worldwide. Several laboratory tests for Map detection are available; however, these are limited by inadequate sensitivity and specificity when used in subclinically infected populations. To identify Map shedders in subclinically infected cattle, we used a new, high-yield method for DNA-extraction from Map in faeces combined with quantitative real-time PCR (qPCR for amplification of the insertion sequence IS900 of Map (HYDEqPCR. Evaluation of HYDEqPCR was carried out in comparison with faecal culture, milk qPCR, and milk enzyme-linked immunosorbent assay (ELISA, on 141 faecal and 91 milk samples, from 141 subclinically infected dairy cattle. Results The qPCR proved to be highly sensitive, with a detection limit of 2 IS900 DNA copies/μl in 67 % of the reactions. It also showed 100 % specificity, as determined from 50 Map and non-Map strains, and by the sequencing of qPCR amplicons. The detection limit of HYDEqPCR was 90 Map/g Map-spiked faeces, which corresponds to 2.4 colony forming units/g Map-spiked faeces, with an estimated efficiency of 85 % (±21 %. When tested on the field samples, HYDEqPCR showed 89 % of the samples as positive for Map, whereas faecal culture, milk qPCR, and milk ELISA detected 19 %, 36 % and 1 %, respectively. Fisher’s exact tests only show statistical significance (p ≤0.05 for the correlation between HYDEqPCR and faecal culture. The agreement between HYDEqPCR and milk qPCR and milk ELISA was poor, slight, and non-significant. Conclusions This study highlights the advantages of HYDEqPCR for detection of Map in subclinically infected populations, in comparison with faecal culture, milk qPCR and milk ELISA. HYDEqPCR can detect low-level Map shedders that go undetected using these other methods, which will thus underestimate the proportions of Map

  16. DNA glue

    DEFF Research Database (Denmark)

    Filichev, Vyacheslav V; Astakhova, Irina V.; Malakhov, Andrei D.


    Significant alterations in thermal stability of parallel DNA triplexes and antiparallel duplexes were observed upon changing the attachment of ethynylpyrenes from para to ortho in the structure of phenylmethylglycerol inserted as a bulge into DNA (TINA). Insertions of two ortho-TINAs as a pseudo...

  17. 含E型沙眼衣原体MOMP基因的重组腺病毒和DNA疫苗联合免疫效果的研究%Immune responses induced by DNA vaccine combined with recombinant adenovirus containing MOMP gene of Chlamydia trachomatis serovar E

    Institute of Scientific and Technical Information of China (English)

    吕慧; 李静; 孙娜; 关冰; 王红; 赵蔚明


      目的探讨E型沙眼衣原体(Ct)主要外膜蛋白(MOMP)DNA疫苗和重组腺病毒联合免疫小鼠诱导的免疫效应。方法构建、纯化重组腺病毒Ad-MOMP及重组真核表达质粒pVAX1-MOMP。设计4种免疫方案,分别为DNA免疫( DNA组)、重组腺病毒免疫( Ad组)、DNA初次免疫-重组腺病毒加强免疫( DNA/Ad组)、重组腺病毒初次免疫-DNA加强免疫( Ad/DNA组)。末次免疫后2周检测小鼠血清特异IgG、IgG1、IgG2a、IgA抗体,阴道分泌物SIgA抗体及脾淋巴细胞分泌IFN-γ、IL-10水平。结果DNA组诱导较弱免疫应答,未产生SIgA抗体及Th1反应。 Ad组诱导出Th1反应及SIgA抗体,且血清抗体显著高于DNA组。联合免疫均能诱导明显强于单独免疫的黏膜SIgA、血清抗体及Th1反应。 Ad/DNA组的Th1反应强于DNA/Ad组;而DNA/Ad组的血清抗体和黏膜抗体水平强于Ad/DNA组。结论Ad-MOMP能诱导黏膜免疫及Th1细胞免疫应答,DNA/Ad及Ad/DNA联合免疫产生的特异性免疫应答明显强于单独免疫。其中Ad/DNA的Th1反应优势更明显,DNA/Ad的血清抗体和黏膜抗体反应更强。接种顺序会影响联合免疫的强弱及类型,这为Ct疫苗的设计研究提供新的思路和实验依据。%Objective To investigate the specific immune responses induced by DNA vaccine com-bined with recombinant adenovirus carrying major outer membrane protein ( MOMP) gene of Chlamydia trachom-atis (Ct) serovar E.Methods Recombinant eukaryotic expression plasmid pVAX 1-MOMP and recombinant adenovirus Ad-MOMP were constructed and purified .Four immunization strategies were designed including DNA immunization (DNA group), recombinant adenovirus immunization (Ad group), DNA prime-recombinant ade-novirus boost regimen ( DNA/Ad group ) and recombinant adenovirus prime-DNA boost regimen ( Ad/DNA group) .Two weeks after the final immunization , vaginal wash specimens , blood samples and spleens were col

  18. Cryptography with DNA binary strands. (United States)

    Leier, A; Richter, C; Banzhaf, W; Rauhe, H


    Biotechnological methods can be used for cryptography. Here two different cryptographic approaches based on DNA binary strands are shown. The first approach shows how DNA binary strands can be used for steganography, a technique of encryption by information hiding, to provide rapid encryption and decryption. It is shown that DNA steganography based on DNA binary strands is secure under the assumption that an interceptor has the same technological capabilities as sender and receiver of encrypted messages. The second approach shown here is based on steganography and a method of graphical subtraction of binary gel-images. It can be used to constitute a molecular checksum and can be combined with the first approach to support encryption. DNA cryptography might become of practical relevance in the context of labelling organic and inorganic materials with DNA 'barcodes'.

  19. PDA: Pooled DNA analyzer

    Directory of Open Access Journals (Sweden)

    Lin Chin-Yu


    Full Text Available Abstract Background Association mapping using abundant single nucleotide polymorphisms is a powerful tool for identifying disease susceptibility genes for complex traits and exploring possible genetic diversity. Genotyping large numbers of SNPs individually is performed routinely but is cost prohibitive for large-scale genetic studies. DNA pooling is a reliable and cost-saving alternative genotyping method. However, no software has been developed for complete pooled-DNA analyses, including data standardization, allele frequency estimation, and single/multipoint DNA pooling association tests. This motivated the development of the software, 'PDA' (Pooled DNA Analyzer, to analyze pooled DNA data. Results We develop the software, PDA, for the analysis of pooled-DNA data. PDA is originally implemented with the MATLAB® language, but it can also be executed on a Windows system without installing the MATLAB®. PDA provides estimates of the coefficient of preferential amplification and allele frequency. PDA considers an extended single-point association test, which can compare allele frequencies between two DNA pools constructed under different experimental conditions. Moreover, PDA also provides novel chromosome-wide multipoint association tests based on p-value combinations and a sliding-window concept. This new multipoint testing procedure overcomes a computational bottleneck of conventional haplotype-oriented multipoint methods in DNA pooling analyses and can handle data sets having a large pool size and/or large numbers of polymorphic markers. All of the PDA functions are illustrated in the four bona fide examples. Conclusion PDA is simple to operate and does not require that users have a strong statistical background. The software is available at

  20. The DNA injury-repair of esophageal cancer EC109 cells to diallyl trisulfide (DATS) combining radiation%二烯丙基三硫化物联合辐射对食管癌EC109细胞DNA损伤及修复影响

    Institute of Scientific and Technical Information of China (English)

    Yang Zhang; Hongbing Ma


    Objective: The aim of our study was to investigate the effect of diallyl trisulfide (DATS) combining radiation on DNA injury-repair of Esophageal cancer EC109 cells. Methods: Using 10 and 20 μg/mL DATS on EC109 cells, and taking X-ray radiation 24 h later. Investigate the radiosensitization effect of DATS on EC109 cells by clone formation, and the mechanism of DNA injury-repair by Comet Assay. Results: The clone formation resulted that DATS had radiosensitization effect on EC109 cells. Radiosensitization enhancement ratios of 10 and 20 μg/mL DATS in combination with radiation were 1.55,1.64 (Do) and 1.43,1.75 (Dq) respectively. In the comet assay, the TM (tail moments) of 20 μg/mL DATS combining radiation group lines at 0 h, 2 h, 6 h and 24 h were 7.16 ± 2.61,3.65 ± 2.06,2.09 ± 0.83,1.45 ± 1.37 respectively. They were slightly increased than radiation group (0.95 ± 0.65, 0.11 ± 0.07, 0.1 ± 0.05, 0.11 ± 0.08) and DATS group (1.81 ± 1.23,1.58 ± 1.40, 0.45 ± 0.25,0.60 ± 0.40) (P < 0.01). The result showed that DATS combining radiation had the effect of increasing DNA damage and inhibiting DNA repair on EC109 cells. Conclusion: DATS has radiosensitization effect on Esophageal cancer EC109 cells. And the effect is probably related with DNA injury-repair.

  1. Human DNA Ligase III Recognizes DNA Ends by Dynamic Switching between Two DNA-Bound States

    Energy Technology Data Exchange (ETDEWEB)

    Cotner-Gohara, Elizabeth; Kim, In-Kwon; Hammel, Michal; Tainer, John A.; Tomkinson, Alan E.; Ellenberger, Tom (Scripps); (Maryland-MED); (WU-MED); (LBNL)


    Human DNA ligase III has essential functions in nuclear and mitochondrial DNA replication and repair and contains a PARP-like zinc finger (ZnF) that increases the extent of DNA nick joining and intermolecular DNA ligation, yet the bases for ligase III specificity and structural variation among human ligases are not understood. Here combined crystal structure and small-angle X-ray scattering results reveal dynamic switching between two nick-binding components of ligase III: the ZnF-DNA binding domain (DBD) forms a crescent-shaped surface used for DNA end recognition which switches to a ring formed by the nucleotidyl transferase (NTase) and OB-fold (OBD) domains for catalysis. Structural and mutational analyses indicate that high flexibility and distinct DNA binding domain features in ligase III assist both nick sensing and the transition from nick sensing by the ZnF to nick joining by the catalytic core. The collective results support a 'jackknife model' in which the ZnF loads ligase III onto nicked DNA and conformational changes deliver DNA into the active site. This work has implications for the biological specificity of DNA ligases and functions of PARP-like zinc fingers.

  2. DNA methylation

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Helin, Kristian


    DNA methylation is involved in key cellular processes, including X-chromosome inactivation, imprinting and transcriptional silencing of specific genes and repetitive elements. DNA methylation patterns are frequently perturbed in human diseases such as imprinting disorders and cancer. The recent...... discovery that the three members of the TET protein family can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) has provided a potential mechanism leading to DNA demethylation. Moreover, the demonstration that TET2 is frequently mutated in haematopoietic tumours suggests that the TET...... proteins are important regulators of cellular identity. Here, we review the current knowledge regarding the function of the TET proteins, and discuss various mechanisms by which they contribute to transcriptional control. We propose that the TET proteins have an important role in regulating DNA methylation...

  3. DNA data (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Raw DNA chromatogram data produced by the ABI 373, 377, 3130 and 3730 automated sequencing machines in ABI format. These are from fish (primarily Sebastes spp.,...

  4. Phylogeny of Deltocephalinae (Hemiptera: Cicadellidae)from China based on partial 16S rDNA and 28S rDNA D2 sequences combined with morphological characters%基于16S rDNA和28S rDNA D2基因序列与形态特征联合分析的中国角顶叶蝉亚科系统发育研究(半翅目:叶蝉科)

    Institute of Scientific and Technical Information of China (English)

    戴仁怀; 陈学新; 李子忠


    The phylogeny of 19 genera of Deltocephalinae leafhoppers was analyzed based on 50 adult morphological characters combined with nucleotide sequences of the mitochondrial 16S rDNA and nuclear 28S D2 rDNA genes. One species of Typhlocybinae was included as outgroup. Parsimonian, distance and Bayesian methods were used to estimate the phylogenetic relationships. The topology of the phylogenetic trees generated with different methods was quite similar. We partially resolved the morphologically-defined tribes and the relationships among 19 genera of Deltocephalinae. The genus Macrosteles was well supported to occupy a basal position in the study, so the most primary tribe in Deltocephalinae might be Macrostelini. The phylogenetic analysis trees put all genera of Deltocephalini but Nakaharanus onto a single lineage. The genus Balclutha, corresponding to the tribe Balclnthini,remains unsolved in our analyses. The Euscelini might be a polyphyletic group in the analysis. Analytical result recovered Athysanini and Paralimnini as monophyletic clades. The clade Phlogotettix and Scaphoideus-Nakaharanus was constantly resolved using different methods. We suggested that Scaphoideus, Nakaharanus and Phlogotettix should be included in or into Scaphoideini. But the results resolved poorly the taxonomic status of Xestoeephalini overall.%首次在国内利用28s rDNA D2区段和16s rDNA基因序列,结合50个形态特征对角顶叶蝉亚科(Deltocephalinae)[半翅目(Hemiptera):叶蝉科(cicadellidae)]19个属进行系统发育分析研究.从无水乙醇浸泡保存的标本中提取基因组DNA并扩增了19个内群和1种外群Tyhlocybinae[半翅目(Hemiptera):叶蝉科(cicadelIidae)]种类的28s rDNA D2基因片段并测序,同时扩增了16s rDNA基因片段并测序11条,采用了GenBank中1个种类的16S rDNA同源序列.采用PAuP*4.O和MrBayes3.0两个分析软件和3种建树方法,利用同源28s D2 rDNA和16srDNA两个基因序列与形态特征结合进行系统发

  5. DNA adductomics. (United States)

    Balbo, Silvia; Turesky, Robert J; Villalta, Peter W


    Systems toxicology is a broad-based approach to describe many of the toxicological features that occur within a living system under stress or subjected to exogenous or endogenous exposures. The ultimate goal is to capture an overview of all exposures and the ensuing biological responses of the body. The term exposome has been employed to refer to the totality of all exposures, and systems toxicology investigates how the exposome influences health effects and consequences of exposures over a lifetime. The tools to advance systems toxicology include high-throughput transcriptomics, proteomics, metabolomics, and adductomics, which is still in its infancy. A well-established methodology for the comprehensive measurement of DNA damage resulting from every day exposures is not fully developed. During the past several decades, the (32)P-postlabeling technique has been employed to screen the damage to DNA induced by multiple classes of genotoxicants; however, more robust, specific, and quantitative methods have been sought to identify and quantify DNA adducts. Although triple quadrupole and ion trap mass spectrometry, particularly when using multistage scanning (LC-MS(n)), have shown promise in the field of DNA adductomics, it is anticipated that high-resolution and accurate-mass LC-MS(n) instrumentation will play a major role in assessing global DNA damage. Targeted adductomics should also benefit greatly from improved triple quadrupole technology. Once the analytical MS methods are fully mature, DNA adductomics along with other -omics tools will contribute greatly to the field of systems toxicology.

  6. Relationship between nucleosome positioning and DNA methylation (United States)

    Chodavarapu, Ramakrishna K.; Feng, Suhua; Bernatavichute, Yana V.; Chen, Pao-Yang; Stroud, Hume; Yu, Yanchun; Hetzel, Jonathan; Kuo, Frank; Kim, Jin; Cokus, Shawn J.; Casero, David; Bernal, Maria; Huijser, Peter; Clark, Amander T.; Krämer, Ute; Merchant, Sabeeha S.; Zhang, Xiaoyu; Jacobsen, Steven E.; Pellegrini, Matteo


    Nucleosomes compact and regulate access to DNA in the nucleus, and are composed of approximately 147 bases of DNA wrapped around a histone octamer1, 2. Here we report a genome-wide nucleosome positioning analysis of Arabidopsis thaliana utilizing massively parallel sequencing of mononucleosomes. By combining this data with profiles of DNA methylation at single base resolution, we identified ten base periodicities in the DNA methylation status of nucleosome-bound DNA and found that nucleosomal DNA was more highly methylated than flanking DNA. These results suggest that nucleosome positioning strongly influences DNA methylation patterning throughout the genome and that DNA methyltransferases preferentially target nucleosome-bound DNA. We also observed similar trends in human nucleosomal DNA suggesting that the relationships between nucleosomes and DNA methyltransferases are conserved. Finally, as has been observed in animals, nucleosomes were highly enriched on exons, and preferentially positioned at intron-exon and exon-intron boundaries. RNA Pol II was also enriched on exons relative to introns, consistent with the hypothesis that nucleosome positioning regulates Pol II processivity. DNA methylation is enriched on exons, consistent with the targeting of DNA methylation to nucleosomes, and suggesting a role for DNA methylation in exon definition. PMID:20512117

  7. 173例系统性红斑狼疮患者ANA、ENA和dsDNA抗体的联合检测分析%Analysis of combined dectection of ANA, ENA and dsDNA in 173 Systemic Lupus Erythematosus patients

    Institute of Scientific and Technical Information of China (English)

    吴希国; 刘秀珍; 马越


    Objective:To evaluate the diagnostic valve of combined detection of ANA, ENA and dsDNA in systemic lupus enythmatosus. Methods; Serum was collected from 173 patients. ANA as well as dsDNA was tested by indirect immunofluorescent method, and ENA was tested by western blot. Results; The detection rates of the three antibodies in female SLE patients were higher than those of male patients. In the serum of patients,the detection rates of ANA, ASA( anti - sm antibodies) and dsDNA were 94. 8% , 32. 2% and 45. 1% respectively. Conclusion; There were significant differences in the sensitivity of ANA, ENA and dsDNA in systemic lupus erythematosus. Combined detection of ANA,ENA and dsDNA autoantibody had the diagnostic value to SLE.%目的:探讨ANA、ENA和dsDNA抗体联合检测在系统性红斑狼疮诊断中的意义.方法:收集173例患者血清,采用间接免疫荧光法检测ANA和dsDNA,用免疫印迹法测定ENA.结果:女性患者三种抗体同时阳性的检出率明显高于男性;患者血清中ANA阳性率为94.8%,抗dsDNA抗体为45.1%,抗Sm抗体为32.2%.结论:ANA、ENA和dsDNA三类抗体在SLE中的敏感性有显著的差异.这三类抗体的联合检测对SLE具有诊断意义.

  8. DNA expressions - A formal notation for DNA

    NARCIS (Netherlands)

    Vliet, Rudy van


    We describe a formal notation for DNA molecules that may contain nicks and gaps. The resulting DNA expressions denote formal DNA molecules. Different DNA expressions may denote the same molecule. Such DNA expressions are called equivalent. We examine which DNA expressions are minimal, which

  9. Impaired NFAT and NFκB activation are involved in suppression of CD40 ligand expression by Δ{sup 9}-tetrahydrocannabinol in human CD4{sup +} T cells

    Energy Technology Data Exchange (ETDEWEB)

    Ngaotepprutaram, Thitirat [Department of Pharmacology and Toxicology, Michigan State University (United States); Center for Integrative Toxicology, Michigan State University (United States); Kaplan, Barbara L.F. [Department of Pharmacology and Toxicology, Michigan State University (United States); Center for Integrative Toxicology, Michigan State University (United States); Neuroscience Program, Michigan State University (United States); Kaminski, Norbert E., E-mail: [Department of Pharmacology and Toxicology, Michigan State University (United States); Center for Integrative Toxicology, Michigan State University (United States)


    We have previously reported that Δ{sup 9}-tetrahydrocannabinol (Δ{sup 9}-THC), the main psychoactive cannabinoid in marijuana, suppresses CD40 ligand (CD40L) expression by activated mouse CD4{sup +} T cells. CD40L is involved in pathogenesis of many autoimmune and inflammatory diseases. In the present study, we investigated the molecular mechanism of Δ{sup 9}-THC-mediated suppression of CD40L expression using peripheral blood human T cells. Pretreatment with Δ{sup 9}-THC attenuated CD40L expression in human CD4{sup +} T cells activated by anti-CD3/CD28 at both the protein and mRNA level, as determined by flow cytometry and quantitative real-time PCR, respectively. Electrophoretic mobility shift assays revealed that Δ{sup 9}-THC suppressed the DNA-binding activity of both NFAT and NFκB to their respective response elements within the CD40L promoter. An assessment of the effect of Δ{sup 9}-THC on proximal T cell-receptor (TCR) signaling induced by anti-CD3/CD28 showed significant impairment in the rise of intracellular calcium, but no significant effect on the phosphorylation of ZAP70, PLCγ1/2, Akt, and GSK3β. Collectively, these findings identify perturbation of the calcium-NFAT and NFκB signaling cascade as a key mechanistic event by which Δ{sup 9}-THC suppresses human T cell function. - Highlights: • Δ{sup 9}-THC attenuated CD40L expression in activated human CD4+ T cells. • Δ{sup 9}-THC suppressed DNA-binding activity of NFAT and NFκB. • Δ{sup 9}-THC impaired elevation of intracellular Ca2+. • Δ{sup 9}-THC did not affect phosphorylation of ZAP70, PLCγ1/2, Akt, and GSK3β.

  10. DNA and RNA sensor

    Institute of Scientific and Technical Information of China (English)

    LIU; Tao; LIN; Lin; ZHAO; Hong; JIANG; Long


    This review summarizes recent advances in DNA sensor. Major areas of DNA sensor covered in this review include immobilization methods of DNA, general techniques of DNA detection and application of nanoparticles in DNA sensor.

  11. What Is Mitochondrial DNA? (United States)

    ... DNA What is mitochondrial DNA? What is mitochondrial DNA? Although most DNA is packaged in chromosomes within ... proteins. For more information about mitochondria and mitochondrial DNA: Molecular Expressions, a web site from the Florida ...

  12. Tetrahedron-structured DNA and functional oligonucleotide for construction of an electrochemical DNA-based biosensor. (United States)

    Bu, Nan-Nan; Tang, Chun-Xia; He, Xi-Wen; Yin, Xue-Bo


    Tetrahedron-structured DNA (ts-DNA) in combination with a functionalized oligonucleotide was used to develop a "turn-on" biosensor for Hg(2+) ions. The ts-DNA provided an improved sensitivity and was used to block the active sites.

  13. DNA vaccines (United States)

    Gregersen, Jens-Peter


    Immunization by genes encoding immunogens, rather than with the immunogen itself, has opened up new possibilities for vaccine research and development and offers chances for new applications and indications for future vaccines. The underlying mechanisms of antigen processing, immune presentation and regulation of immune responses raise high expectations for new and more effective prophylactic or therapeutic vaccines, particularly for vaccines against chronic or persistent infectious diseases and tumors. Our current knowledge and experience of DNA vaccination is summarized and critically reviewed with particular attention to basic immunological mechanisms, the construction of plasmids, screening for protective immunogens to be encoded by these plasmids, modes of application, pharmacokinetics, safety and immunotoxicological aspects. DNA vaccines have the potential to accelerate the research phase of new vaccines and to improve the chances of success, since finding new immunogens with the desired properties is at least technically less demanding than for conventional vaccines. However, on the way to innovative vaccine products, several hurdles have to be overcome. The efficacy of DNA vaccines in humans appears to be much less than indicated by early studies in mice. Open questions remain concerning the persistence and distribution of inoculated plasmid DNA in vivo, its potential to express antigens inappropriately, or the potentially deleterious ability to insert genes into the host cell's genome. Furthermore, the possibility of inducing immunotolerance or autoimmune diseases also needs to be investigated more thoroughly, in order to arrive at a well-founded consensus, which justifies the widespread application of DNA vaccines in a healthy population.

  14. DNA nanotechnology

    Directory of Open Access Journals (Sweden)

    Nadrian C Seeman


    We are all aware that the DNA found in cells is a double helix consisting of two antiparallel strands held together by specific hydrogen-bonded base pairs; adenine (A always pairs with thymine (T, and guanine (G always pairs with cytosine (C. The specificity of this base pairing and the ability to ensure that it occurs in this fashion (and not some other1 is key to the use of DNA in materials applications. The double helical arrangement of the two molecules leads to a linear helix axis, linear not in the geometrical sense of being a straight line, but in the topological sense of being unbranched. Genetic engineers discovered in the 1970s how to splice together pieces of DNA to add new genes to DNA molecules2, and synthetic chemists worked out convenient syntheses for short pieces of DNA (up to ∼100–150 units in the 1980s3. Regardless of the impact of these technologies on biological systems, hooking together linear molecules leads only to longer linear molecules, with circles, knots, and catenanes perhaps resulting from time to time.

  15. Ancient DNA from marine mammals

    DEFF Research Database (Denmark)

    Foote, Andrew David; Hofreiter, Michael; Morin, Philip A


    such as bone, tooth, baleen, skin, fur, whiskers and scrimshaw using ancient DNA (aDNA) approaches provide an oppor- tunity for investigating such changes over evolutionary and ecological timescales. Here, we review the application of aDNA techniques to the study of marine mammals. Most of the studies have...... focused on detecting changes in genetic diversity following periods of exploitation and environmental change. To date, these studies have shown that even small sample sizes can provide useful information on historical genetic diversity. Ancient DNA has also been used in investigations of changes...... in distribution and range of marine mammal species; we review these studies and discuss the limitations of such ‘presence only’ studies. Combining aDNA data with stable isotopes can provide further insights into changes in ecology and we review past studies and suggest future potential applications. We also...

  16. Structural organization of DNA in chlorella viruses.

    Directory of Open Access Journals (Sweden)

    Timo Wulfmeyer

    Full Text Available Chlorella viruses have icosahedral capsids with an internal membrane enclosing their large dsDNA genomes and associated proteins. Their genomes are packaged in the particles with a predicted DNA density of ca. 0.2 bp nm(-3. Occasionally infection of an algal cell by an individual particle fails and the viral DNA is dynamically ejected from the capsid. This shows that the release of the DNA generates a force, which can aid in the transfer of the genome into the host in a successful infection. Imaging of ejected viral DNA indicates that it is intimately associated with proteins in a periodic fashion. The bulk of the protein particles detected by atomic force microscopy have a size of ∼60 kDa and two proteins (A278L and A282L of about this size are among 6 basic putative DNA binding proteins found in a proteomic analysis of DNA binding proteins packaged in the virion. A combination of fluorescence images of ejected DNA and a bioinformatics analysis of the DNA reveal periodic patterns in the viral DNA. The periodic distribution of GC rich regions in the genome provides potential binding sites for basic proteins. This DNA/protein aggregation could be responsible for the periodic concentration of fluorescently labeled DNA observed in ejected viral DNA. Collectively the data indicate that the large chlorella viruses have a DNA packaging strategy that differs from bacteriophages; it involves proteins and share similarities to that of chromatin structure in eukaryotes.

  17. DNA: Polymer and molecular code (United States)

    Shivashankar, G. V.


    The thesis work focusses upon two aspects of DNA, the polymer and the molecular code. Our approach was to bring single molecule micromanipulation methods to the study of DNA. It included a home built optical microscope combined with an atomic force microscope and an optical tweezer. This combined approach led to a novel method to graft a single DNA molecule onto a force cantilever using the optical tweezer and local heating. With this method, a force versus extension assay of double stranded DNA was realized. The resolution was about 10 picoN. To improve on this force measurement resolution, a simple light backscattering technique was developed and used to probe the DNA polymer flexibility and its fluctuations. It combined the optical tweezer to trap a DNA tethered bead and the laser backscattering to detect the beads Brownian fluctuations. With this technique the resolution was about 0.1 picoN with a millisecond access time, and the whole entropic part of the DNA force-extension was measured. With this experimental strategy, we measured the polymerization of the protein RecA on an isolated double stranded DNA. We observed the progressive decoration of RecA on the l DNA molecule, which results in the extension of l , due to unwinding of the double helix. The dynamics of polymerization, the resulting change in the DNA entropic elasticity and the role of ATP hydrolysis were the main parts of the study. A simple model for RecA assembly on DNA was proposed. This work presents a first step in the study of genetic recombination. Recently we have started a study of equilibrium binding which utilizes fluorescence polarization methods to probe the polymerization of RecA on single stranded DNA. In addition to the study of material properties of DNA and DNA-RecA, we have developed experiments for which the code of the DNA is central. We studied one aspect of DNA as a molecular code, using different techniques. In particular the programmatic use of template specificity makes

  18. Use of sperm plasmid DNA lipofection combined with REMI (restriction enzyme-mediated insertion) for production of transgenic chickens expressing eGFP (enhanced green fluorescent protein) or human follicle-stimulating hormone. (United States)

    Harel-Markowitz, Eliane; Gurevich, Michael; Shore, Laurence S; Katz, Adi; Stram, Yehuda; Shemesh, Mordechai


    Linearized p-eGFP (plasmid-enhanced green fluorescent protein) or p-hFSH (plasmid human FSH) sequences with the corresponding restriction enzyme were lipofected into sperm genomic DNA. Sperm transfected with p-eGFP were used for artificial insemination in hens, and in 17 out of 19 of the resultant chicks, the exogenous DNA was detected in their lymphocytes as determined by PCR and expressed in tissues as determined by (a) PCR, (b) specific emission of green fluorescence by the eGFP, and (c) Southern blot analysis. A complete homology was found between the Aequorea Victoria eGFP DNA and a 313-bp PCR product of extracted DNA from chick blood cells. Following insemination with sperm lipofected with p-hFSH, transgenic offspring were obtained for two generations as determined by detection of the transgene for human FSH (PCR) and expression of the gene (RT-PCR and quantitative real-time PCR) and the presence of the protein in blood (radioimmunoassay). Data demonstrate that lipofection of plasmid DNA with restriction enzyme is a highly efficient method for the production of transfected sperm to produce transgenic offspring by direct artificial insemination.

  19. Combined Targeted DNA Sequencing in Non-Small Cell Lung Cancer (NSCLC Using UNCseq and NGScopy, and RNA Sequencing Using UNCqeR for the Detection of Genetic Aberrations in NSCLC.

    Directory of Open Access Journals (Sweden)

    Xiaobei Zhao

    Full Text Available The recent FDA approval of the MiSeqDx platform provides a unique opportunity to develop targeted next generation sequencing (NGS panels for human disease, including cancer. We have developed a scalable, targeted panel-based assay termed UNCseq, which involves a NGS panel of over 200 cancer-associated genes and a standardized downstream bioinformatics pipeline for detection of single nucleotide variations (SNV as well as small insertions and deletions (indel. In addition, we developed a novel algorithm, NGScopy, designed for samples with sparse sequencing coverage to detect large-scale copy number variations (CNV, similar to human SNP Array 6.0 as well as small-scale intragenic CNV. Overall, we applied this assay to 100 snap-frozen lung cancer specimens lacking same-patient germline DNA (07-0120 tissue cohort and validated our results against Sanger sequencing, SNP Array, and our recently published integrated DNA-seq/RNA-seq assay, UNCqeR, where RNA-seq of same-patient tumor specimens confirmed SNV detected by DNA-seq, if RNA-seq coverage depth was adequate. In addition, we applied the UNCseq assay on an independent lung cancer tumor tissue collection with available same-patient germline DNA (11-1115 tissue cohort and confirmed mutations using assays performed in a CLIA-certified laboratory. We conclude that UNCseq can identify SNV, indel, and CNV in tumor specimens lacking germline DNA in a cost-efficient fashion.

  20. Roles of 1,25(OH2D3 and Vitamin D Receptor in the Pathogenesis of Rheumatoid Arthritis and Systemic Lupus Erythematosus by Regulating the Activation of CD4+ T Cells and the PKCδ/ERK Signaling Pathway

    Directory of Open Access Journals (Sweden)

    Xiao-Jie He


    Full Text Available Background/Aims: The study aims to elucidate the roles of 1,25(OH2D3 and vitamin D receptor (VDR in the pathogenesis of rheumatoid arthritis (RA and systemic lupus erythematosus (SLE by regulating the activation of CD4+ T cells and the PKCδ/ERK signaling pathway. Methods: From January 2013 to December 2015, a total of 130 SLE patients, 137 RA patients and 130 healthy controls were selected in this study. Serum levels of 1,25(OH2D3 and VDR mRNA expression were detected by ELISA and real-time fluorescence quantitative PCR (RT-qPCR. Density gradient centrifugation was performed to separate peripheral blood mononuclear cells (PBMCs. CD4+ T cells were separated using magnetic activated cell sorting (MACS. CD4+T cells in logarithmic growth phase were collected and assigned into 9 groups: the normal control group, the normal negative control (NC group, the VDR siRNA group, the RA control group, the RA NC group, the VDR over-expressed RA group, the SLE control group, the SLE NC group, and the VDR over-expressed SLE group. The mRNA and protein expressions of VDR, PKCδ, ERK1/2, CD11a, CD70 and CD40L were detected by RT-qPCR and Western blotting. Bisulfite genomic sequencing was conducted to monitor the methylation status of CD11a, CD70 and CD40L. Results: Compared with healthy controls, serum 1,25(OH2D3 level and VDR mRNA expression in peripheral blood were decreased in SLE patients and RA patients. With the increase of concentrations of 1,25(OH2D3 treatment, the VDR mRNA expression and DNA methylation levels of CD11a, CD70 and CD40L were declined, while the expressions of PKCδ, ERK1/2, CD11a, CD70 and CD40L were elevated in SLE, RA and normal CD4+T cells. Compared with the SLE contro, RA control, SLE NC and RA NC groups, the expressions of PKCδ, ERK1/2, CD11a, CD70 and CD40L decreased but DNA methylation levels of CD11a, CD70 and CD40L increased in the VDR over-expressed SLE group and VDR over-expressed RA group. However, compared with the normal

  1. The application of combination detection of hepatitis B serological markers quantifi-cation and HBV DNA quantification in the diagnosis of hepatitis B virus infection%乙肝血清学标志物定量和HBV DNA定量联合检测在乙肝病毒感染诊断中的应用

    Institute of Scientific and Technical Information of China (English)

    吴洪秋; 张永良; 黄坚尧; 张汉运


    Objective To analyze the application value of combination detection in the diagnosis of hepatitis B virus ( HBV) infection by the quantitative detection of serological markers and HBV DNA of hepatitis B patients. Methods The serum samples of 120 hepatitis B patients from Jun. 2013 to Jun. 2015 were collected, and the ELISA qualitative test and RT-PCR were used to detect the contents of HBV serological markers ( HBsAg, anti-HBs, HBeAg, anti-HBe, anti-HBc) and HBV DNA. Results The HBV DNA positive rate was 96. 15% in Ⅰ group; the HBV DNA positive rate was 48. 08% in Ⅱ group;the HBV DNA positive rate was 4. 76% inⅢgroup. The quantitative HBV DNA inⅠgroup was significantly higher than that in Ⅱ and Ⅲ groups ( P0. 05). Conclusion The combination detection of HBV serological markers and HBV DNA quantification plays a complementary role in the diagnosis of HBV infection, and has a more accurate diagnosis as well as can provide a more effective reference.%目的:分析乙肝患者的血清标志物和乙肝病毒( HBV) DNA联合检测在HBV感染诊断中的应用价值。方法以2013年6月-2015年6月在珠海市妇幼保健院就诊的120例乙肝患者血清样本作为研究资料,分别采用ELISA定性试验和实时荧光定量PCR( RT-PCR)检测HBV血清标志物( HBsAg、抗-HBs、HBeAg、抗-HBe、抗-HBc)和HBV DNA含量。结果Ⅰ组HBV DNA阳性率为96.15%;Ⅱ组HBV DNA阳性率为48.08%;Ⅲ组HBV DNA阳性率为4.76%。Ⅰ组HBV DNA定量显著高于Ⅱ、Ⅲ两组( P0.05)。结论乙肝血清标志物定量与HBV DNA定量联合检测在诊断HBV感染过程中起互相补充的作用,诊断结果更加准确,可提供更有效的参考依据。

  2. Studies on the induction of Epstein-Barr virus (EBV) DNA polymerase (POL) and deoxyribonuclease (DNase) by the combined action of 12-O-tetradecanoyl-phorbol-13-acetate (TPA) and N-butyrate (SB in EBV-carrying cells

    Energy Technology Data Exchange (ETDEWEB)

    Nutter, L.M.; Tan, R.S.; Grill, S.; Li, J.S.; Cheng, Y.C.


    TPA and SB were found to induce EBV early antigen in EBV-carrying Raji cells, a Burkitt's Lymphoma-derived human cell line. The mode of interaction of these agents was unclear. They have examined the induction of EBV-POL and DNase activities by TPA and SB. It was found that neither agent alone could induce EBV-POL and DNase activities, even though the virus DNA could be induced by either compound alone. Induction of virus enzymes could only occur when cells were exposed to both compounds. A 2h exposure to TPA followed by 46h to SB resulted in levels of induction of EBV-POL and DNase activities comparable to those induced with simultaneous exposure to both agents for 48h. No induction of the enzymes will occur if the sequence of exposure to these agents is reversed. Phospholipase C, which increases intracellular diacylglycerol (and subsequently the activation of Protein Kinase C), and 5-Aza-deoxycytidine, a DNA hypomethylating agent, were able to partially substitute for TPA and SB, respectively. These results suggest that the mechanism of induction of EBV enzyme activities by TPA and SB could involve both Protein Kinase C activation and DNA hypomethylation. Furthermore, the synthesis of EBV DNA is not sufficient for induction of these virus enzyme activities.

  3. HIV DNA Vaccine: Stepwise Improvements Make a Difference

    Directory of Open Access Journals (Sweden)

    Barbara K. Felber


    Full Text Available Inefficient DNA delivery methods and low expression of plasmid DNA have been major obstacles for the use of plasmid DNA as vaccine for HIV/AIDS. This review describes successful efforts to improve DNA vaccine methodology over the past ~30 years. DNA vaccination, either alone or in combination with other methods, has the potential to be a rapid, safe, and effective vaccine platform against AIDS. Recent clinical trials suggest the feasibility of its translation to the clinic.

  4. Analysis of the Framework of Microsoft DNA

    Institute of Scientific and Technical Information of China (English)


    Microsoft DNA(Distributed interNet Application) has p rovided a effective framework of combination PC with the Internet perfectly; In addition, this open framework hase also given the integration of multilingual co mponents a strong managing platform. This article has deeply analysed the main technologys of Microsoft DNA, involve COM basic technology, framework of DNA, Microfost UDA(Universal Data Access),com ponent management with COM+, asynchronous communication with MSMQ(M icrosoft Message Queue). In...

  5. Sorting fluorescent nanocrystals with DNA

    Energy Technology Data Exchange (ETDEWEB)

    Gerion, Daniele; Parak, Wolfgang J.; Williams, Shara C.; Zanchet, Daniela; Micheel, Christine M.; Alivisatos, A. Paul


    Semiconductor nanocrystals with narrow and tunable fluorescence are covalently linked to oligonucleotides. These biocompounds retain the properties of both nanocrystals and DNA. Therefore, different sequences of DNA can be coded with nanocrystals and still preserve their ability to hybridize to their complements. We report the case where four different sequences of DNA are linked to four nanocrystal samples having different colors of emission in the range of 530-640 nm. When the DNA-nanocrystal conjugates are mixed together, it is possible to sort each type of nanoparticle using hybridization on a defined micrometer -size surface containing the complementary oligonucleotide. Detection of sorting requires only a single excitation source and an epifluorescence microscope. The possibility of directing fluorescent nanocrystals towards specific biological targets and detecting them, combined with their superior photo-stability compared to organic dyes, opens the way to improved biolabeling experiments, such as gene mapping on a nanometer scale or multicolor microarray analysis.

  6. DNA condensation in one dimension (United States)

    Pardatscher, Günther; Bracha, Dan; Daube, Shirley S.; Vonshak, Ohad; Simmel, Friedrich C.; Bar-Ziv, Roy H.


    DNA can be programmed to assemble into a variety of shapes and patterns on the nanoscale and can act as a template for hybrid nanostructures such as conducting wires, protein arrays and field-effect transistors. Current DNA nanostructures are typically in the sub-micrometre range, limited by the sequence space and length of the assembled strands. Here we show that on a patterned biochip, DNA chains collapse into one-dimensional (1D) fibres that are 20 nm wide and around 70 µm long, each comprising approximately 35 co-aligned chains at its cross-section. Electron beam writing on a photocleavable monolayer was used to immobilize and pattern the DNA molecules, which condense into 1D bundles in the presence of spermidine. DNA condensation can propagate and split at junctions, cross gaps and create domain walls between counterpropagating fronts. This system is inherently adept at solving probabilistic problems and was used to find the possible paths through a maze and to evaluate stochastic switching circuits. This technique could be used to propagate biological or ionic signals in combination with sequence-specific DNA nanotechnology or for gene expression in cell-free DNA compartments.

  7. Does the tautomeric status of the adenine bases change upon the dissociation of the A*·A(syn) Topal-Fresco DNA mismatch? A combined QM and QTAIM atomistic insight. (United States)

    Brovarets', Ol'ha O; Zhurakivsky, Roman O; Hovorun, Dmytro M


    We have scrupulously explored the tautomerisation mechanism via the double proton transfer of the A*·A(syn) Topal-Fresco base mispair (C(s) symmetry), formed by the imino and amino tautomers of the adenine DNA base in the anti- and syn-conformations, respectively, bridging quantum-mechanical calculations with Bader's quantum theory of atoms in molecules. It was found that the A*·A(syn) ↔ A·A*(syn) tautomerisation is the asynchronous concerted process. It was established that the A*·A(syn) DNA mismatch is stabilized by the N6H···N6 (6.35) and N1H···N7 (6.17) hydrogen (H) bonds, whereas the A·A*(syn) base mispair (Cs) by the N6H···N6 (8.82) and N7H···N1 (9.78) H-bonds and the C8H···HC2 HH-bond (0.30 kcal mol(-1)). Using the sweeps of the energies of the intermolecular H-bonds, it was observed that the N6H···N6 and N1H···N7/N7H···N1 H-bonds are anti-cooperative and mutually weaken each other in the A*·A(syn) and A·A*(syn) mispairs. It was revealed that the A·A*(syn) DNA mismatch is a dynamically unstable structure with a short lifetime of 1.12 × 10(-13) s and any of its 6 low-frequency intermolecular vibrations can develop during this period of time. This observation makes it impossible to change the tautomeric status of the A bases upon the dissociation of the A*·A(syn) base mispair into the monomers during DNA replication.

  8. Detection of Non-Amplified Genomic DNA

    CERN Document Server

    Corradini, Roberto


    This book offers a state-of-the-art overview on non amplified DNA detection methods and provides chemists, biochemists, biotechnologists and material scientists with an introduction to these methods. In fact all these fields have dedicated resources to the problem of nucleic acid detection, each contributing with their own specific methods and concepts. This book will explain the basic principles of the different non amplified DNA detection methods available, highlighting their respective advantages and limitations. The importance of non-amplified DNA sequencing technologies will be also discussed. Non-amplified DNA detection can be achieved by adopting different techniques. Such techniques have allowed the commercialization of innovative platforms for DNA detection that are expected to break into the DNA diagnostics market. The enhanced sensitivity required for the detection of non amplified genomic DNA has prompted new strategies that can achieve ultrasensitivity by combining specific materials with specifi...

  9. 基于 DNA 条形码-产地-形态分析联用的巴西草药 CENTELHA ASIÁTICA(积雪草)的生药学研究%The pharmaceutical research on Brazilian herb CENTELHA ASIÁTICA(Centella asiatica) based on a combined analysis of DNA barcoding-origin-morphology

    Institute of Scientific and Technical Information of China (English)

    顾选; 李妍芃; 崔秀梅; 王娟; 韩丽; 赵百孝; 刘春生; 马长华; 崔馨云


    目的:对巴西草药 CENTELHA ASIÁTICA 进行生药学研究。方法采用 DNA 条形码技术对巴西草药的叶片提取 DNA、扩增 ITS 序列、双向测序,采用相似度法进行物种鉴定,再结合产地信息和性状特征核对 DNA 条形码鉴定结果进行验证。结果巴西草药 CENTELHA ASIÁTICA 与NCBI 核酸数据库积雪草 ITS 序列达到最高相似度,相似度为99%,鉴定其为伞形科植物积雪草Centella asiatica(L.) Urban。在地理分布上,巴西草药 CENTELHA ASIÁTICA 符合积雪草的分布特征;从形态分析上,样品与积雪草特征相符合。结论基于 DNA 条形码-产地-形态分析的鉴定方法能够对巴西草药 CENTELHA ASIÁTICA 进行鉴定,鉴定该物种来源于伞形科植物积雪草 Centella asiatica(L.) Urban 的干燥全草。生药学研究能够为 CENTELHA ASIÁTICA 品种鉴定及质量标准研究提供依据。%Objective To study Brazilian herbal CENTELHA ASIÁTICA from the perspective of bi-ological pharmacy. Methods By applying DNA barcoding technology, total genomic DNA was isolated from the materials, and nuclear DNA ITS sequences were amplified and sequenced;DNA fragments were collated and matched by using ContingExpress. Similarity identification of BLAST analysis was performed. Next, the DNA bar code was verified by the information of plant origin and morphology. Families and genera were identified by Molecular identification. Results ITS sequence of Brazil herb CENTELHA ASIÁTICA and Centella asiatica (L. ) Urban was 99% identical. The results can be solidified by their sim-ilarities in geographical distribution and morphological features. Conclusion Based on DNA barcoding-origin-morphological analysis Brazilian herbal CENTELHA ASIÁTICA was identified as Centella asiatica L. and biological pharmacy can provide the basis for the identification and quality standard of CENTELHA ASIÁTICA varieties.

  10. Functionalizing Designer DNA Crystals (United States)

    Chandrasekaran, Arun Richard

    Three-dimensional crystals have been self-assembled from a DNA tensegrity triangle via sticky end interaction. The tensegrity triangle is a rigid DNA motif containing three double helical edges connected pair-wise by three four-arm junctions. The symmetric triangle contains 3 unique strands combined in a 3:3:1 ratio: 3 crossover, 3 helical and 1 central. The length of the sticky end reported previously was two nucleotides (nt) (GA:TC) and the motif with 2-helical turns of DNA per edge diffracted to 4.9 A at beam line NSLS-X25 and to 4 A at beam line ID19 at APS. The purpose of these self-assembled DNA crystals is that they can be used as a framework for hosting external guests for use in crystallographic structure solving or the periodic positioning of molecules for nanoelectronics. This thesis describes strategies to improve the resolution and to incorporate guests into the 3D lattice. The first chapter describes the effect of varying sticky end lengths and the influence of 5'-phosphate addition on crystal formation and resolution. X-ray diffraction data from beam line NSLS-X25 revealed that the crystal resolution for 1-nt (G:C) sticky end was 3.4 A. Motifs with every possible combination of 1-nt and 2-nt sticky-ended phosphorylated strands were crystallized and X-ray data were collected. The position of the 5'-phosphate on either the crossover (strand 1), helical (strand 2), or central strand (3) had an impact on the resolution of the self-assembled crystals with the 1-nt 1P-2-3 system diffracting to 2.62 A at APS and 3.1 A at NSLS-X25. The second chapter describes the sequence-specific recognition of DNA motifs with triplex-forming oligonucleotides (TFOs). This study examined the feasibility of using TFOs to bind to specific locations within a 3-turn DNA tensegrity triangle motif. The TFO 5'-TTCTTTCTTCTCT was used to target the tensegrity motif containing an appropriately embedded oligopurine.oligopyrimidine binding site. As triplex formation involving cytidine

  11. Soluble CD40 ligand is elevated in type 1 diabetic nephropathy but not predictive of mortality, cardiovascular events or kidney function. (United States)

    Lajer, Maria; Tarnow, Inge; Michelson, Alan D; Jorsal, Anders; Frelinger, Andrew L; Parving, Hans-Henrik; Rossing, Peter; Tarnow, Lise


    Soluble CD40 ligand (sCD40L) derived from platelets mediates atherothrombosis, leading to proinflammatory and proatherosclerotic responses. We investigated the predictive value of plasma sCD40L for all-cause mortality, cardiovascular mortality and morbidity, progression towards end-stage renal disease (ESRD) and rate of decline in glomerular filtration rate (GFR) in patients with type 1 diabetes (T1DM) and nephropathy. The study was a prospective, observational follow-up study of 443 T1DM patients with diabetic nephropathy (274 men; age 42.1 ± 10.5 years [mean ± SD], duration of diabetes 28.3 ± 8.9 years, GFR 76 ± 33 ml/min/1.73 m2) and a control group of 421 patients with longstanding type 1 diabetes and persistent normoalbuminuria (232 men; age 45.4 ± 11.5 years, duration of diabetes 27.7 ± 10.1 years) at baseline. sCD40L was measured by ELISA. Plasma sCD40L levels were higher in patients with diabetic nephropathy compared to normoalbuminuric patients (median (range) 1.54 (0.02-13.38) vs. 1.30 (0.04-20.65) µg/L, respectively p = 0.004). The patients were followed for 8.1 (0.0-12.9) years (median (range)). Among normoalbuminuric patients, sCD40L levels did not predict all-cause mortality (p = 0.33) or combined fatal and non-fatal cardiovascular disease (CVD) (p = 0.27). Similarly, among patients with diabetic nephropathy, the covariate adjusted sCD40L levels did not predict all-cause mortality (p = 0.86) or risk of fatal and non-fatal CVD (p = 0.08). Furthermore, high levels of sCD40L did not predict development of ESRD (p = 0.85) nor rate of decline in GFR (p = 0.69). Plasma sCD40L is elevated in T1DM nephropathy but is not a predictor of all-cause mortality, cardiovascular mortality and morbidity or deterioration of kidney function

  12. Synthesis and structure elucidation of new μ-oxamido-bridged dicopper(II) complex with in vitro anticancer activity: A combined study from experiment verification and docking calculation on DNA/protein-binding property. (United States)

    Zhu, Ling; Zheng, Kang; Li, Yan-Tuan; Wu, Zhi-Yong; Yan, Cui-Wei


    A new oxamido-bridged dicopper(II) complex with formula of [Cu2(deap)(pic)2], where H2deap and pic represent N,N'-bis[3-(diethylamino)propyl]oxamide and picrate, respectively, was synthesized and characterized by elemental analyses, molar conductance measurements, IR and electronic spectral study, and single-crystal X-ray diffraction. The crystal structure analyses revealed that the two copper(II) atoms in the dicopper(II) complex are bridged by the trans-deap(2-) ligand with the distances of 5.2116(17)Å, and the coordination environment around the copper(II) atoms can be described as a square-planar geometry. Hydrogen bonding and π-π stacking interactions link the dicopper(II) complex into a three-dimensional infinite network. The DNA/protein-binding properties of the complex are investigated by molecular docking and experimental assays. The results indicate that the dicopper(II) complex can interact with HS-DNA in the mode of intercalation and effectively quench the intrinsic fluorescence of protein BSA by 1:1 binding with the most possible binding site in the proximity of Trp134. The in vitro anticancer activities suggest that the complex is active against the selected tumor cell lines, and IC50 values for SMMC-7721 and HepG2 are lower than cisplatin. The effects of the electron density distribution of the terminal ligand and the chelate ring arrangement around copper(II) ions bridged by symmetric N,N'-bis(substituted)oxamides on DNA/BSA-binding ability and in vitro anticancer activity are preliminarily discussed.

  13. DNA nanostructure meets nanofabrication. (United States)

    Zhang, Guomei; Surwade, Sumedh P; Zhou, Feng; Liu, Haitao


    Recent advances in DNA nanotechnology have made it possible to construct DNA nanostructures of almost arbitrary shapes with 2-3 nm of precision in their dimensions. These DNA nanostructures are ideal templates for bottom-up nanofabrication. This review highlights the challenges and recent advances in three areas that are directly related to DNA-based nanofabrication: (1) fabrication of large scale DNA nanostructures; (2) pattern transfer from DNA nanostructure to an inorganic substrate; and (3) directed assembly of DNA nanostructures.

  14. Analysis of differentially expressed tumor-related genes in Peutz-Jeghers syndrome combined with colorectal carcinoma with cDNA microarrays%对比分析黑斑息肉综合征合并大肠癌组织肿瘤基因

    Institute of Scientific and Technical Information of China (English)

    Xiaosan Zhu; Qiaofang Sang; Xiaojuan Zhan; Yichen Dai; Qingzhen Nan; Zhangxin Chen; Junpei Xie; Wei Zeng; Yuka Fu; Yuanyuan Lin; Qingna Lian


    Objective: The aim of the study was to screen the differentially expressed genes of Peutz-Jeghers syndrome (PJS) and colorectal carcinoma (CRC). Methods: This study used cDNA microarray to comparatively analyze the gene expression profiles of 4 cases of PJS combined with colorectal adenocarcinoma vs. normal mucosae. The cDNA microarray contained 8064 human genes, and then using RT-PCR to test three genes of all. Results: The experimental data showed that fourteen genes were differentially expressed, which were up-regulated in PJS. Fifty-one genes expressions were altered in CRCs, of which 32 were up-regulated, as compared to the normal mucosae. In addition, 5 genes were similarly altered in both PJS and CRCs. RT-PCR analyses confirmed the cDNA microarray data for three of those genes: LATS2, APC and MADH4. Conclusion: LCN2, USP4, GRO3, HYAL1 and APC - these differentially expressed genes likely represent biomarkers for early detection of CRC and may be potential therapeutic targets.

  15. Pig transgenesis by Sleeping Beauty DNA transposition

    DEFF Research Database (Denmark)

    Jakobsen, Jannik E.; Li, Juan; Kragh, Peter M.


    disease models. In this report, we present transgenic pigs created by Sleeping Beauty DNA transposition in primary porcine fibroblasts in combination with somatic cell nuclear transfer by handmade cloning. Göttingen minipigs expressing green fluorescent protein are produced by transgenesis with DNA...... plasmid DNA. Our findings illustrate critical issues related to DNA transposon-directed transgenesis, including coincidental plasmid insertion and relatively low Sleeping Beauty transposition activity in porcine fibroblasts, but also provide a platform for future development of porcine disease models...... using the Sleeping Beauty gene insertion technology....

  16. DNA detection using recombination proteins.

    Directory of Open Access Journals (Sweden)

    Olaf Piepenburg


    Full Text Available DNA amplification is essential to most nucleic acid testing strategies, but established techniques require sophisticated equipment or complex experimental procedures, and their uptake outside specialised laboratories has been limited. Our novel approach, recombinase polymerase amplification (RPA, couples isothermal recombinase-driven primer targeting of template material with strand-displacement DNA synthesis. It achieves exponential amplification with no need for pretreatment of sample DNA. Reactions are sensitive, specific, and rapid and operate at constant low temperature. We have also developed a probe-based detection system. Key aspects of the combined RPA amplification/detection process are illustrated by a test for the pathogen methicillin-resistant Staphylococcus aureus. The technology proves to be sensitive to fewer than ten copies of genomic DNA. Furthermore, products can be detected in a simple sandwich assay, thereby establishing an instrument-free DNA testing system. This unique combination of properties is a significant advance in the development of portable and widely accessible nucleic acid-based tests.

  17. Research on the source of varieties and high performance liquid chromatography of Brazilian herb BARDANA based on a combined analysis of DNA barcoding-origin-morphology%基于 DNA 条形码-产地-形态分析联用的巴西草药 BARDANA(牛蒡)的品种鉴定及高效液相色谱研究

    Institute of Scientific and Technical Information of China (English)

    余春霞; 顾选; 李妍芃; 肖瑶; 赵百孝; 刘春生; 马长华; 韩丽


    Objective To trace the source and study on the content of arctiin of Brazilian herb BARDANA for varieties systematics and pharmacological analysis. Methods The source of varieties of Brazilian herb BARDANA was identified by a technology combined DNA barcoding, plant geographical origin and morphological features , and the content of arctiin was analyzed by HPLC. Results DNA barcoding preliminarily identified BARDANA belongs to the stretch of Arctium of Compositae with a similarity level of 99% . Geographical and morphological verification further confirmed the aforementioned finding. The content of arctiin in the Brazilian was 0. 281% ,which was significantly lower than the Chinese arctiin (3. 72% ). Conclusion Brazilian herb BARDANA derives from Arctium lappa L. , and the content of arctiin was very low.%目的:对巴西草药牛蒡的品种进行鉴定,同时研究其中的牛蒡苷含量,为其品种整理和药理研究提供依据。方法利用 DNA 条形码—产地—形态分析联用技术鉴定巴西草药牛蒡的基原,高效液相色谱法测定其牛蒡苷含量。结果 DNA 条形码初步鉴定巴西草药牛蒡为菊科牛蒡属植物,且与牛蒡达到最高相似度99%,产地及形态分析进一步确证其为牛蒡的地上部分;巴西牛蒡草中牛蒡苷平均含量为0.281%,明显低于中国牛蒡草牛蒡苷平均含量3.72%。结论巴西草药牛蒡来源于牛蒡 Arctium lappa L.的干燥地上部分,其牛蒡苷含量极低。

  18. Clinical trial in healthy malaria-naïve adults to evaluate the safety, tolerability, immunogenicity and efficacy of MuStDO5, a five-gene, sporozoite/hepatic stage Plasmodium falciparum DNA vaccine combined with escalating dose human GM-CSF DNA (United States)

    Richie, Thomas L.; Charoenvit, Yupin; Wang, Ruobing; Epstein, Judith E.; Hedstrom, Richard C.; Kumar, Sanjai; Luke, Thomas C.; Freilich, Daniel A.; Aguiar, Joao C.; Sacci, Jr., John B.; Sedegah, Martha; Nosek, Jr., Ronald A.; De La Vega, Patricia; Berzins, Mara P.; Majam, Victoria F.; Abot, Esteban N.; Ganeshan, Harini; Richie, Nancy O.; Banania, Jo Glenna; Baraceros, Maria Fe B.; Geter, Tanya G.; Mere, Robin; Bebris, Lolita; Limbach, Keith; Hickey, Bradley W.; Lanar, David E.; Ng, Jennifer; Shi, Meng; Hobart, Peter M.; Norman, Jon A.; Soisson, Lorraine A.; Hollingdale, Michael R.; Rogers, William O.; Doolan, Denise L.; Hoffman, Stephen L.


    When introduced in the 1990s, immunization with DNA plasmids was considered potentially revolutionary for vaccine development, particularly for vaccines intended to induce protective CD8 T cell responses against multiple antigens. We conducted, in 1997−1998, the first clinical trial in healthy humans of a DNA vaccine, a single plasmid encoding Plasmodium falciparum circumsporozoite protein (PfCSP), as an initial step toward developing a multi-antigen malaria vaccine targeting the liver stages of the parasite. As the next step, we conducted in 2000–2001 a clinical trial of a five-plasmid mixture called MuStDO5 encoding pre-erythrocytic antigens PfCSP, PfSSP2/TRAP, PfEXP1, PfLSA1 and PfLSA3. Thirty-two, malaria-naïve, adult volunteers were enrolled sequentially into four cohorts receiving a mixture of 500 μg of each plasmid plus escalating doses (0, 20, 100 or 500 μg) of a sixth plasmid encoding human granulocyte macrophage-colony stimulating factor (hGM-CSF). Three doses of each formulation were administered intramuscularly by needle-less jet injection at 0, 4 and 8 weeks, and each cohort had controlled human malaria infection administered by five mosquito bites 18 d later. The vaccine was safe and well-tolerated, inducing moderate antigen-specific, MHC-restricted T cell interferon-γ responses but no antibodies. Although no volunteers were protected, T cell responses were boosted post malaria challenge. This trial demonstrated the MuStDO5 DNA and hGM-CSF plasmids to be safe and modestly immunogenic for T cell responses. It also laid the foundation for priming with DNA plasmids and boosting with recombinant viruses, an approach known for nearly 15 y to enhance the immunogenicity and protective efficacy of DNA vaccines. PMID:23151451

  19. Combined detection of sputum smears ,sputum TB-DNA and serum anti-PPD-IgG in diagnosis of tuberculosis%痰涂片和TB-DNA及血清抗PPD-IgG在肺结核感染诊断中的联合应用

    Institute of Scientific and Technical Information of China (English)



    目的 探讨痰 TB-DNA 定性与血清抗结核抗体及痰抗酸染色检测方法在肺结核感染诊断中的联合应用价值.方法 以2013年1月至2015年6月在清远市人民医院就诊的肺结核患者278例为研究对象.另择性别、年龄匹配的同期入院非肺结核病患者121例为对照组.现通过收集该肺结核患者的TB-DNA定性和血清抗结核抗体及抗酸染色的检测结果进行分析 ,探讨痰TB-DNA定性与血清抗结核抗体检测及抗酸染色在肺结核感染诊断中的联合应用.结果 结核病组中抗酸染色灵敏度为32 .01% ;血清抗结核抗体灵敏度为51 .44% ;TB-DNA定性灵敏度为48 .56% ;TB-DNA定性和血清抗结核抗体联合检出率为67 .63% ;TB-DNA定性和抗酸染色联合检出率为54 .68% ;血清抗结核抗体和抗酸染色联合检出率为57 .55% ;三者联合检出率为68 .71% .结论 血清抗结核抗体检测对肺结核的诊断简单、有效 ,灵敏度优于TB-DNA定性检测及抗酸染色 ,但其特异度比较低.细菌学诊断是结核病诊断的"金标准" ,但是痰涂片寻找抗酸杆菌的阳性率低 ,而 TB-DNA定性检测快速又准确.血清抗结核抗体及痰抗酸染色及痰TB-DNA定性检测联合应用于肺结核诊断效果更佳.%Objective To explore the value of combined application of qualitative detection of TB-DNA serum anti-PPD-IgG and acid-fast staining methods in the diagnosis of tuberculosis infection .Methods Totally 278 pulmonary tuberculosis patients and 121 non-pulmonary tuberculosis patients were collected from Qingyuan people′s hospital during the period from January 2013 to June 2015 .Tuberculosis in patients with TB-DNA qualitative and serum anti-PPD-IgG and acid-fast staining test results was analyzed . Sputum TB-DNA qualitative and serum anti-PPD-IgG detection and joint application of acid-fast staining in the diagnosis of tuber-culosis infection .Results Sensitivities of acid-fast staining ,TB-DNA and serum anti

  20. DNA-scaffolded nanoparticle structures

    Energy Technology Data Exchange (ETDEWEB)

    Hoegberg, Bjoern; Olin, Haakan [Department of Engineering Physics and Mathematics, Mid Sweden University, SE-851 70 Sundsvall, Sweden (Sweden)


    DNA self-assembly is a powerful route to the production of very small, complex structures. When used in combination with nanoparticles it is likely to become a key technology in the production of nanoelectronics in the future. Previously, demonstrated nanoparticle assemblies have mainly been periodic and highly symmetric arrays, unsuited as building blocks for any complex circuits. With the invention of DNA-scaffolded origami reported earlier this year (Rothemund P W K 2006 Nature 440 (7082) 297-302), a new route to complex nanostructures using DNA has been opened. Here, we give a short review of the field and present the current status of our experiments were DNA origami is used in conjunction with nanoparticles. Gold nanoparticles are functionalized with thiolated single stranded DNA. Strands that are complementary to the gold particle strands can be positioned on the self-assembled DNA-structure in arbitrary patterns. This property should allow an accurate positioning of the particles by letting them hybridize on the lattice. We report on our recent experiments on this system and discuss open problems and future applications.

  1. DNA barcoding methods for land plants. (United States)

    Fazekas, Aron J; Kuzmina, Maria L; Newmaster, Steven G; Hollingsworth, Peter M


    DNA barcoding in the land plants presents a number of challenges compared to DNA barcoding in many animal clades. The CO1 animal DNA barcode is not effective for plants. Plant species hybridize frequently, and there are many cases of recent speciation via mechanisms, such as polyploidy and breeding system transitions. Additionally, there are many life-history trait combinations, which combine to reduce the likelihood of a small number of markers effectively tracking plant species boundaries. Recent results, however, from the two chosen core plant DNA barcode regions rbcL and matK plus two supplementary regions trnH-psbA and internal transcribed spacer (ITS) (or ITS2) have demonstrated reasonable levels of species discrimination in both floristic and taxonomically focused studies. We describe sampling techniques, extraction protocols, and PCR methods for each of these two core and two supplementary plant DNA barcode regions, with extensive notes supporting their implementation for both low- and high-throughput facilities.

  2. DNA-based cryptographic methods for data hiding in DNA media. (United States)

    Marwan, Samiha; Shawish, Ahmed; Nagaty, Khaled


    Information security can be achieved using cryptography, steganography or a combination of them, where data is firstly encrypted using any of the available cryptography techniques and then hid into any hiding medium. Recently, the famous genomic DNA has been introduced as a hiding medium, known as DNA steganography, due to its notable ability to hide huge data sets with a high level of randomness and hence security. Despite the numerous cryptography techniques, to our knowledge only the vigenere cipher and the DNA-based playfair cipher have been combined with the DNA steganography, which keeps space for investigation of other techniques and coming up with new improvements. This paper presents a comprehensive analysis between the DNA-based playfair, vigenere, RSA and the AES ciphers, each combined with a DNA hiding technique. The conducted analysis reports the performance diversity of each combined technique in terms of security, speed, hiding capacity in addition to both key size and data size. Moreover, this paper proposes a modification of the current combined DNA-based playfair cipher technique, which makes it not only simple and fast but also provides a significantly higher hiding capacity and security. The conducted extensive experimental studies confirm such outstanding performance in comparison with all the discussed combined techniques.

  3. A Phase I Double Blind, Placebo-Controlled, Randomized Study of the Safety and Immunogenicity of Electroporated HIV DNA with or without Interleukin 12 in Prime-Boost Combinations with an Ad35 HIV Vaccine in Healthy HIV-Seronegative African Adults.

    Directory of Open Access Journals (Sweden)

    Juliet Mpendo

    Full Text Available Strategies to enhance the immunogenicity of DNA vaccines in humans include i co-administration of molecular adjuvants, ii intramuscular administration followed by in vivo electroporation (IM/EP and/or iii boosting with a different vaccine. Combining these strategies provided protection of macaques challenged with SIV; this clinical trial was designed to mimic the vaccine regimen in the SIV study.Seventy five healthy, HIV-seronegative adults were enrolled into a phase 1, randomized, double-blind, placebo-controlled trial. Multi-antigenic HIV (HIVMAG plasmid DNA (pDNA vaccine alone or co-administered with pDNA encoding human Interleukin 12 (IL-12 (GENEVAX IL-12 given by IM/EP using the TriGrid Delivery System was tested in different prime-boost regimens with recombinant Ad35 HIV vaccine given IM.All local reactions but one were mild or moderate. Systemic reactions and unsolicited adverse events including laboratory abnormalities did not differ between vaccine and placebo recipients. No serious adverse events (SAEs were reported. T cell and antibody response rates after HIVMAG (x3 prime-Ad35 (x1 boost were independent of IL-12, while the magnitude of interferon gamma (IFN-γ ELISPOT responses was highest after HIVMAG (x3 without IL-12. The quality and phenotype of T cell responses shown by intracellular cytokine staining (ICS were similar between groups. Inhibition of HIV replication by autologous T cells was demonstrated after HIVMAG (x3 prime and was boosted after Ad35. HIV specific antibodies were detected only after Ad35 boost, although there was a priming effect with 3 doses of HIVMAG with or without IL-12. No anti-IL-12 antibodies were detected.The vaccines were safe, well tolerated and moderately immunogenic. Repeated administration IM/EP was well accepted. An adjuvant effect of co-administered plasmid IL-12 was not NCT01496989.

  4. DNA ligase I, the replicative DNA ligase. (United States)

    Howes, Timothy R L; Tomkinson, Alan E


    Multiple DNA ligation events are required to join the Okazaki fragments generated during lagging strand DNA synthesis. In eukaryotes, this is primarily carried out by members of the DNA ligase I family. The C-terminal catalytic region of these enzymes is composed of three domains: a DNA binding domain, an adenylation domain and an OB-fold domain. In the absence of DNA, these domains adopt an extended structure but transition into a compact ring structure when they engage a DNA nick, with each of the domains contacting the DNA. The non-catalytic N-terminal region of eukaryotic DNA ligase I is responsible for the specific participation of these enzymes in DNA replication. This proline-rich unstructured region contains the nuclear localization signal and a PCNA interaction motif that is critical for localization to replication foci and efficient joining of Okazaki fragments. DNA ligase I initially engages the PCNA trimer via this interaction motif which is located at the extreme N-terminus of this flexible region. It is likely that this facilitates an additional interaction between the DNA binding domain and the PCNA ring. The similar size and shape of the rings formed by the PCNA trimer and the DNA ligase I catalytic region when it engages a DNA nick suggest that these proteins interact to form a double-ring structure during the joining of Okazaki fragments. DNA ligase I also interacts with replication factor C, the factor that loads the PCNA trimeric ring onto DNA. This interaction, which is regulated by phosphorylation of the non-catalytic N-terminus of DNA ligase I, also appears to be critical for DNA replication.

  5. Protection against SHIV-KB9 Infection by Combining rDNA and rFPV Vaccines Based on HIV Multiepitope and p24 Protein in Chinese Rhesus Macaques

    Directory of Open Access Journals (Sweden)

    Chang Li


    Full Text Available Developing an effective vaccine against HIV infection remains an urgent goal. We used a DNA prime/fowlpox virus boost regimen to immunize Chinese rhesus macaques. The animals were challenged intramuscularly with pathogenic molecularly cloned SHIV-KB9. Immunogenicity and protective efficacy of vaccines were investigated by measuring IFN-γ levels, monitoring HIV-specific binding antibodies, examining viral load, and analyzing CD4/CD8 ratio. Results show that, upon challenge, the vaccine group can induce a strong immune response in the body, represented by increased expression of IFN-γ, slow and steady elevated antibody production, reduced peak value of acute viral load, and increase in the average CD4/CD8 ratio. The current research suggests that rapid reaction speed, appropriate response strength, and long-lasting immune response time may be key protection factors for AIDS vaccine. The present study contributes significantly to AIDS vaccine and preclinical research.

  6. 乙肝不同血清模式及乙肝DNA定量与前S1抗原联合检测的临床意义%Clinical values of combined analysis on serological patterns, virus DNA titer and pre-S1 antigen for hepatitis B

    Institute of Scientific and Technical Information of China (English)

    王凤敏; 李志


    目的 探讨乙型肝炎患者不同的血清学模式、乙肝病毒DNA(HBV-DNA)与乙肝前S1抗原(Pre-S1 Ag)联合检测的临床意义.方法 采用化学免疫发光法(CLIA)定量筛选339例乙肝血清标志物阳性血清,采用荧光定量聚合酶链反应法(FQ-PCR)检测HBV-DNA,采用酶联免疫吸附法(ELISA)检测Pre-S1 Ag.结果 乙肝不同血清模式下,HBV-DNA与Pre-S1 Ag检测结果比较差异无统计学意义(P>0.05).HBsAg、HBeAg、抗-HBc阳性组HBV-DNA检出率93.1%,Pre-S1Ag检出率86.1%.HBsAg、HBeAb、抗-HBc阳性组HBV-DNA检出率45.9%,Pre-S1 Ag检出率69.2%.HBsAg、抗-HBc阳性组HBV-DNA检出率61.0%,Pre-S1 Ag检出率72.9%.HBsAg、HBeAg阳性组HBV-DNA及Pre-S1 Ag检出率均为100%.以HBeAg阳性为对照HBV-DNA及Pre-S1 Ag检出率分别为87.3%和93.7%.HBV-DNA与Pre-S1 Ag检测结果比较差异有统计学意义(P>0.05).结论 乙肝五项、HBV-DNA、Pre-S1Ag联合检测能够对乙肝病毒的感染、复制程度做出准确的判断,为临床治疗方案的选择和疗效的观察提供可靠的依据.%Objective To discuss clinical values of the combined analysis on serological patterns, virus DNA titer and pre-S1 antigen for hepatitis B.Methods Serum samples from 339 patients with chemical luminescent immunoassay (CLIA) positive results were used in the study.The level of serum HBV-DNA was detected by fluorescent quantitative polymerase chain reaction (FQ-PCR).Pre-S1Ag was detected by ELISA.Results There was no significant differences in pre-S1 Ag or HBV-DNA with different serological patterns of hepatitis B (P > 0.05).The HBV-DNA positive rate of the HBsAg, HBeAg and Anti-HBc positive group was 93.1% while the pre-S1Ag positive rate was 86.1%.The HBV-DNA positive rate of the HB-sAg, HBeAb, anti-HBc positive group was 45.9% and the Pre-S1Ag positive rate was 69.2%.The HBV-DNA positive rate of the HBsAg, anti-HBc positive groups was 61.0%.The Pre-S1Ag positive rate was 72.9

  7. Augmentation of protein production by a combination of the T7 RNA polymerase system and ubiquitin fusion: Overproduction of the human DNA repair protein, ERCC1, as a ubiquitin fusion protein in Escherichia coli.

    NARCIS (Netherlands)

    M.H.M. Koken (Marcel); J.H. Odijk; M. van Duin (Mark); M.W.J. Fornerod (Maarten); D. Bootsma (Dirk); J.H.J. Hoeijmakers (Jan)


    textabstractThis article presents the development of a set of new expression vectors for overproduction of proteins in Escherichia coli. The vectors, pETUBI-ES1, 2 and 3, allow in-frame cloning of any sequence with the ubiquitin gene driven by the strong T7f10 promoter. Combination of the T7 express

  8. Combination analysis. (United States)

    Tallarida, Ronald J


    This chapter describes quantitative methodology that is directed toward assessing interactions between a combination of agonist drugs that individually produce overtly similar effects. Drugs administered in combination may show exaggerated, reduced or predictable effects that are dependent on the specific drug pair and the doses of t h e constituents. The basisfor quantitating these unusual interactions is the concept of dose equivalence which, in turn, is determined from the individual drug dose-effect relations. A common analytical procedure that follows from dose equivalence uses a graph termed an isobologram. We present here an overview of the isobologram, its use and certain related methods that apply to classifying various drug interactions.

  9. Aptamer-Binding Directed DNA Origami Pattern for Logic Gates. (United States)

    Yang, Jing; Jiang, Shuoxing; Liu, Xiangrong; Pan, Linqiang; Zhang, Cheng


    In this study, an aptamer-substrate strategy is introduced to control programmable DNA origami pattern. Combined with DNA aptamer-substrate binding and DNAzyme-cutting, small DNA tiles were specifically controlled to fill into the predesigned DNA origami frame. Here, a set of DNA logic gates (OR, YES, and AND) are performed in response to the stimuli of adenosine triphosphate (ATP) and cocaine. The experimental results are confirmed by AFM imaging and time-dependent fluorescence changes, demonstrating that the geometric patterns are regulated in a controllable and programmable manner. Our approach provides a new platform for engineering programmable origami nanopatterns and constructing complex DNA nanodevices.

  10. Synthesis of DNA (United States)

    Mariella, Jr., Raymond P.


    A method of synthesizing a desired double-stranded DNA of a predetermined length and of a predetermined sequence. Preselected sequence segments that will complete the desired double-stranded DNA are determined. Preselected segment sequences of DNA that will be used to complete the desired double-stranded DNA are provided. The preselected segment sequences of DNA are assembled to produce the desired double-stranded DNA.

  11. DNA-Protected Silver Clusters for Nanophotonics

    Directory of Open Access Journals (Sweden)

    Elisabeth Gwinn


    Full Text Available DNA-protected silver clusters (AgN-DNA possess unique fluorescence properties that depend on the specific DNA template that stabilizes the cluster. They exhibit peak emission wavelengths that range across the visible and near-IR spectrum. This wide color palette, combined with low toxicity, high fluorescence quantum yields of some clusters, low synthesis costs, small cluster sizes and compatibility with DNA are enabling many applications that employ AgN-DNA. Here we review what is known about the underlying composition and structure of AgN-DNA, and how these relate to the optical properties of these fascinating, hybrid biomolecule-metal cluster nanomaterials. We place AgN-DNA in the general context of ligand-stabilized metal clusters and compare their properties to those of other noble metal clusters stabilized by small molecule ligands. The methods used to isolate pure AgN-DNA for analysis of composition and for studies of solution and single-emitter optical properties are discussed. We give a brief overview of structurally sensitive chiroptical studies, both theoretical and experimental, and review experiments on bringing silver clusters of distinct size and color into nanoscale DNA assemblies. Progress towards using DNA scaffolds to assemble multi-cluster arrays is also reviewed.

  12. Trapping and manipulating single molecules of DNA (United States)

    Shon, Min Ju

    This thesis presents the development and application of nanoscale techniques to trap and manipulate biomolecules, with a focus on DNA. These methods combine single-molecule microscopy and nano- and micro-fabrication to study biophysical properties of DNA and proteins. The Dimple Machine is a lab-on-a-chip device that can isolate and confine a small number of molecules from a bulk solution. It traps molecules in nanofabricated chambers, or "dimples", and the trapped molecules are then studied on a fluorescence microscope at the single-molecule level. The sampling of bulk solution by dimples is representative, reproducible, and automated, enabling highthroughput single-molecule experiments. The device was applied to study hybridization of oligonucleotides, particularly in the context of reaction thermodynamics and kinetics in nanoconfinement. The DNA Pulley is a system to study protein binding and the local mechanical properties of DNA. A molecule of DNA is tethered to a surface on one end, and a superparamagnetic bead is attached to the other. A magnet pulls the DNA taut, and a silicon nitride knife with a nanoscale blade scans the DNA along its contour. Information on the local properties of the DNA is extracted by tracking the bead with nanometer precision in a white-light microscope. The system can detect proteins bound to DNA and localize their recognition sites, as shown with a model protein, EcoRI restriction enzyme. Progress on the measurements of nano-mechanical properties of DNA is included.

  13. Tomato protoplast DNA transformation : physical linkage and recombination of exogenous DNA sequences

    NARCIS (Netherlands)

    Jongsma, Maarten; Koornneef, Maarten; Zabel, Pim; Hille, Jacques


    Tomato protoplasts have been transformed with plasmid DNA's, containing a chimeric kanamycin resistance gene and putative tomato origins of replication. A calcium phosphate-DNA mediated transformation procedure was employed in combination with either polyethylene glycol or polyvinyl alcohol. There w

  14. Electrochemical DNA sandwich assay with a lipase label for attomole detection of DNA

    DEFF Research Database (Denmark)

    Ferapontova, Elena; Hansen, Majken Nørgaard; Saunders, Aaron Marc


    A fast and sensitive electrochemical lipase-based sandwich hybridization assay for detection of attomole levels of DNA has been developed. A combination of magnetic beads, used for pre-concentration and bioseparation of the analyte with a lipase catalyst label allowed detection of DNA with a limit...

  15. Affinity purification of sequence-specific DNA binding proteins.



    We describe a method for affinity purification of sequence-specific DNA binding proteins that is fast and effective. Complementary chemically synthesized oligodeoxynucleotides that contain a recognition site for a sequence-specific DNA binding protein are annealed and ligated to give oligomers. This DNA is then covalently coupled to Sepharose CL-2B with cyanogen bromide to yield the affinity resin. A partially purified protein fraction is combined with competitor DNA and subsequently passed t...

  16. Combination rules

    NARCIS (Netherlands)

    Holicky, M.; Vrouwenvelder, A.C.W.M.


    Load combinations specified in EN 1990 for verification of ultimate limit and serviceability limit states in conjunction with the partial factor method are discussed and illustrated by practical examples of typical civil structures. Alternative procedures to identify critical load cases are reviewed

  17. 天门地区152例系统性红斑狼疮患者血清ANA、抗dsDNA抗体和抗ENA抗体联合检测分析%Analysis of combined detection of ANA, anti dsDNA antibody and anti ENA antibody in 152 patients with systemic lupus erythematosus serum in Tianmen area

    Institute of Scientific and Technical Information of China (English)



    ObjectiveTo evaluate the diagnostic valve of combined detection of ANA, anti-dsDNA antibody and anti-ENA antibody in systemic lupus enythmatosus (SLE).MethodFrom April 2012 to April 2015, 152 SLE patients (SLE group) and 85 healthy people (control group) in our hospital were examined and compared. ANA was tested by indirect immumolfuorescence method; anti dsDNA antibody was tested by dot-immunogold filtration assay; anti-ENA antibody was tested by immunoblotting.ResultThe positive rate of combined detection in SLE group was signiifcantly higher than control group (P<0.01). The positive rates of ANA, anti-dsDNA antibody and anti-ENA antibody in SLE group were higher than control group (P<0.05). Among anti-ENA antibody repertoire, the positive rate of anti-SS-A antibody was the highest. The anti-dsDNA positive rate of LN group was higher than NLN group (P<0.05). The proportion of women with autoantibodies was signiifcantly higher than that of men (P<0.01), and the highest positive rate was 56 to 65 years old.Conclusion Combined detection of ANA, anti-dsDNA and anti-ENA antibody has some clinical value of early diagnosis of SLE. Combined testing will help improve the detection rate, and there are signiifcant differences in positive rates of different gender and age of the patients.%目的:探讨联合检测血清抗核抗体(ANA)、抗双链DNA(dsDNA)抗体和抗可提取性核抗原(ENA)抗体对系统性红斑狼疮(SLE)的诊断价值。方法分别采用间接免疫荧光法、胶体金斑点渗滤法、免疫印迹法检测并分析本院2012年4月至2015年4月收治的152例SLE患者(SLE组)与同期85例健康者(对照组)的ANA、抗dsDNA抗体、抗ENA抗体。结果 SLE组患者三种抗体联合检测的阳性率明显高于对照组(P<0.01),且ANA、抗dsDNA抗体、抗ENA抗体的阳性率均明显高于对照组(P<0.05)。在抗ENA抗体谱中,抗SS-A抗体的阳性率最高。狼疮性肾炎(LN)组的

  18. Mechanism of DNA loading by the DNA repair helicase XPD. (United States)

    Constantinescu-Aruxandei, Diana; Petrovic-Stojanovska, Biljana; Penedo, J Carlos; White, Malcolm F; Naismith, James H


    The xeroderma pigmentosum group D (XPD) helicase is a component of the transcription factor IIH complex in eukaryotes and plays an essential role in DNA repair in the nucleotide excision repair pathway. XPD is a 5' to 3' helicase with an essential iron-sulfur cluster. Structural and biochemical studies of the monomeric archaeal XPD homologues have aided a mechanistic understanding of this important class of helicase, but several important questions remain open. In particular, the mechanism for DNA loading, which is assumed to require large protein conformational change, is not fully understood. Here, DNA binding by the archaeal XPD helicase from Thermoplasma acidophilum has been investigated using a combination of crystallography, cross-linking, modified substrates and biochemical assays. The data are consistent with an initial tight binding of ssDNA to helicase domain 2, followed by transient opening of the interface between the Arch and 4FeS domains, allowing access to a second binding site on helicase domain 1 that directs DNA through the pore. A crystal structure of XPD from Sulfolobus acidocaldiarius that lacks helicase domain 2 has an otherwise unperturbed structure, emphasizing the stability of the interface between the Arch and 4FeS domains in XPD.

  19. Mechanism of DNA loading by the DNA repair helicase XPD (United States)

    Constantinescu-Aruxandei, Diana; Petrovic-Stojanovska, Biljana; Penedo, J. Carlos; White, Malcolm F.; Naismith, James H.


    The xeroderma pigmentosum group D (XPD) helicase is a component of the transcription factor IIH complex in eukaryotes and plays an essential role in DNA repair in the nucleotide excision repair pathway. XPD is a 5′ to 3′ helicase with an essential iron–sulfur cluster. Structural and biochemical studies of the monomeric archaeal XPD homologues have aided a mechanistic understanding of this important class of helicase, but several important questions remain open. In particular, the mechanism for DNA loading, which is assumed to require large protein conformational change, is not fully understood. Here, DNA binding by the archaeal XPD helicase from Thermoplasma acidophilum has been investigated using a combination of crystallography, cross-linking, modified substrates and biochemical assays. The data are consistent with an initial tight binding of ssDNA to helicase domain 2, followed by transient opening of the interface between the Arch and 4FeS domains, allowing access to a second binding site on helicase domain 1 that directs DNA through the pore. A crystal structure of XPD from Sulfolobus acidocaldiarius that lacks helicase domain 2 has an otherwise unperturbed structure, emphasizing the stability of the interface between the Arch and 4FeS domains in XPD. PMID:26896802

  20. The improvement of liposome-mediated transfection of pEGFP DNA into human prostate cancer cells by combining low-frequency and low-energy ultrasound with microbubbles. (United States)

    Bai, Wen-Kun; Wu, Zuo-Hui; Shen, E; Zhang, Ji-Zhen; Hu, Bing


    The aim of this study was to explore the use of a contrast agent to study the effects of exposure to ultrasound, in combination with microbubbles, on liposome-mediated transfection of genes into human prostate cancer cells. A contrast agent was used to study the effects of ultrasound exposure in combination with microbubbles on liposomes, which transfect genes into human prostate cancer cells. The human prostate cancer cell line PC-3 in suspension was exposed to ultrasound with a 20% duty cycle (i.e., 2 sec 'on' time and 8 sec 'off' time) lasting 5 min, with and without ultrasound contrast agent (SonoVue™) using a digital sonifier at a frequency of 21 kHz and an intensity of 4.6 mW/cm2. Immediately after exposure to ultrasound, cell viability and membrane damage were measured. After exposure to ultrasound, the cell suspensions were put into 12‑well plates and cultured for 24 h. Fluorescence microscopy and flow cytometry were used to detect pEGFP transfection efficiency. Exposure to ultrasound alone and ultrasound combined with microbubbles resulted in minimal cell death and induced negligible cell membrane damage. Ultrasound combined with microbubbles had a greater effect on cell membrane damage in all groups: the average cell membrane damage was 41.87%, and it was approximately 42‑fold greater than in the control group. The average transfection efficiency of PC-3 cells was 20.30% for the liposome (Lipofectamine™)+pEGFP+ultrasound+ultrasound contrast agent (SonoVue) group; this was the highest rate of all groups measured and was approximately 81‑fold greater than that of the control group. The use of low-frequency and low-energy ultrasound, in combination with microbubbles, could be a potent physical method for increasing liposome gene delivery efficiency. This technique is a promising non-viral approach that can be used in prostate cancer gene therapy.

  1. Molecular DNA switches and DNA chips (United States)

    Sabanayagam, Chandran R.; Berkey, Cristin; Lavi, Uri; Cantor, Charles R.; Smith, Cassandra L.


    We present an assay to detect single-nucleotide polymorphisms on a chip using molecular DNA switches and isothermal rolling- circle amplification. The basic principle behind the switch is an allele-specific oligonucleotide circularization, mediated by DNA ligase. A DNA switch is closed when perfect hybridization between the probe oligonucleotide and target DNA allows ligase to covalently circularize the probe. Mismatches around the ligation site prevent probe circularization, resulting in an open switch. DNA polymerase is then used to preferentially amplify the closed switches, via rolling-circle amplification. The stringency of the molecular switches yields 102 - 103 fold discrimination between matched and mismatched sequences.

  2. Natural transformation of bacteria by fragmented, damaged and ancient DNA

    DEFF Research Database (Denmark)

    Overballe-Petersen, Søren

    Organisms release DNA both when they live and die. Eventually the DNA disintegrates entirely or it is re-metabolized. There is a constant deposition and decomposition that maintains an environmental pool with large quantities of extracellular DNA, some of which can be thousands of years old...... it by damaged short DNA with abasic sites, crosslinks, and miscoding lesions, which are the most common damages in environmental DNA. This is emphasized by successful natural transformation by 43,000-year-old DNA. We find that the process is a simple variant of natural transformation. On top, we illustrate...... acquire functional genetic signatures of the deeper past. Moreover, not only can old DNA revert microbes to past genotypes, but damaged DNA can also produce new variants of already functional sequences. Besides, DNA fragments carry potential to combine functional domains in new ways. The identified novel...

  3. Autonomous Generation and Loading of DNA Guides by Bacterial Argonaute. (United States)

    Swarts, Daan C; Szczepaniak, Malwina; Sheng, Gang; Chandradoss, Stanley D; Zhu, Yifan; Timmers, Elizabeth M; Zhang, Yong; Zhao, Hongtu; Lou, Jizhong; Wang, Yanli; Joo, Chirlmin; van der Oost, John


    Several prokaryotic Argonaute proteins (pAgos) utilize small DNA guides to mediate host defense by targeting invading DNA complementary to the DNA guide. It is unknown how these DNA guides are being generated and loaded onto pAgo. Here, we demonstrate that guide-free Argonaute from Thermus thermophilus (TtAgo) can degrade double-stranded DNA (dsDNA), thereby generating small dsDNA fragments that subsequently are loaded onto TtAgo. Combining single-molecule fluorescence, molecular dynamic simulations, and structural studies, we show that TtAgo loads dsDNA molecules with a preference toward a deoxyguanosine on the passenger strand at the position opposite to the 5' end of the guide strand. This explains why in vivo TtAgo is preferentially loaded with guides with a 5' end deoxycytidine. Our data demonstrate that TtAgo can independently generate and selectively load functional DNA guides.

  4. Copper(II) complexes of salicylic acid combining superoxide dismutase mimetic properties with DNA binding and cleaving capabilities display promising chemotherapeutic potential with fast acting in vitro cytotoxicity against cisplatin sensitive and resistant cancer cell lines. (United States)

    O'Connor, Mark; Kellett, Andrew; McCann, Malachy; Rosair, Georgina; McNamara, Mary; Howe, Orla; Creaven, Bernadette S; McClean, Siobhán; Kia, Agnieszka Foltyn-Arfa; O'Shea, Denis; Devereux, Michael


    The complexes [Cu(salH)(2)(H(2)O)] (1), [Cu(dipsH)(2)(H(2)O)] (2), {Cu(3-MeOsal)(H(2)O)(0.75)}(n) (3), [Cu(dipsH)(2)(BZDH)(2)] (4), [Cu(dipsH)(2)(2-MeOHBZDH)(2)]·EtOH (5), [Cu(sal)(phen)] (6), [Cu(dips)(phen)]·H(2)O (7), and [Cu(3-MeOsal)(phen)]·H(2)O (8) (salH(2) = salicylic acid; dipsH(2) = 3,5-diisopropylsalicylic acid; 3-MeOsalH(2) = 3-methoxysalicylic acid; BZDH = benzimidazole; 2-MeOHBZDH = 2 methanolbenzimidazole and phen =1,10-phenanthroline) were prepared and characterized. Structures of 4, 5, and 8 were determined by X-ray crystallography. Compounds 1-8 are potent superoxide dismutase mimetics, and they are inactive as inhibitors of COX-2 activity. Compounds 1, 4, and 5 exhibit moderate inhibition of COX-1. Complexes 6-8 display rapid micromolar cytotoxicity against cisplatin sensitive (breast (MCF-7), prostate (DU145), and colon (HT29)) and cisplatin resistant (ovarian (SK-OV-3)) cell lines compared to 1-5, and they exhibit potent in vitro DNA binding and cleavage capabilities.

  5. 用RACE结合cDNA文库筛选的方法获取新的锌指蛋白基因%Isolation of New Zinc Finger Genes through cDNA Library Screening Combined with RACE

    Institute of Scientific and Technical Information of China (English)

    杜占文; 刘立仁; 张俊武



  6. The detection of HBV DNA G1896A point mutation with locked nucleic acid technology combined with molecular beacon%锁核酸结合分子信标技术检测乙型肝炎病毒DNA G1896A点突变研究

    Institute of Scientific and Technical Information of China (English)

    张红; 郑欣; 宋庆涛; 蔡剑英; 王大明; 曾劲峰; 叶贤林; 熊文


    Objective The aim of this study is to investigate and evaluate the real-time fluorescent PCR detection method of hepatitis B virus (HBV) DNA G1896A point mutations. Methods A total of 158 HBV samples which had been analyzed for G1896A mutation were selected, including 150 non-mutation samples and 58 mutant samples. The molecular beacon probe was designed in the mutant region, and the sample was processed with locked nucleic acid in the point mutation region. The pre C region G1896A point mutations of HBV was detected with Fluorescent PCR, then use DNA sequencing to confirm 8 mutant samples, 6 heterozygous samples, and 19 non-mutation samples which had been detected by real-time fluorescent PCR detection method. Results (l)Both the sensitivity of mutant plasmids and of wild-type plasmids achieved 100 copies/ml. (2)There was no detection signal when we used mutant probe to detect the high concentration of wild-type plasmids. It was the same when we used wild-type probe to detect the high concentration of mutant plasmids. (3)The mutant could be detected when the mutational template accounted for 5% of the total heterozygous. (4)All the result of detection with sequencing coincided with that of detection with real-time fluorescent PCR detection method. Conclusion Because real-time fluorescent PCR detection method can rapidly, easily, and exactly detect the HBV DNA G1896A point mutation, thus it is an important method to detect point mutations and has important clinical value.%目的 研究和评估乙型肝炎病毒(HBV)DNA G1896A点突变的实时荧光PCR检测方法.方法 收集经测序验证HBV DNA G1896A未突变的野生型样本150例和已发生突变的突变型样本58例,在突变区域设计分子信标探针,点突变处进行锁核酸处理,利用荧光PCR方法检测HBV前C区G1896A点突变;再从临床标本中随机抽取18例、8例和19例荧光PCR结果分别显示为G1896A突变的标本、杂合的标本以及野生型的标本的PCR

  7. Combination Light (United States)


    The Rayovac TANDEM is an advanced technology combination work light and general purpose flashlight that incorporates several NASA technologies. The TANDEM functions as two lights in one. It features a long range spotlight and wide angle floodlight; simple one-hand electrical switching changes the beam from spot to flood. TANDEM developers made particular use of NASA's extensive research in ergonomics in the TANDEM's angled handle, convenient shape and different orientations. The shatterproof, water resistant plastic casing also draws on NASA technology, as does the shape and beam distance of the square diffused flood. TANDEM's heavy duty magnet that permits the light to be affixed to any metal object borrows from NASA research on rare earth magnets that combine strong magnetic capability with low cost. Developers used a NASA-developed ultrasonic welding technique in the light's interior.

  8. Combining haplotypers

    CERN Document Server

    Kääriäinen, Matti; Lappalainen, Sampsa; Mielikäinen, Taneli


    Statistically resolving the underlying haplotype pair for a genotype measurement is an important intermediate step in gene mapping studies, and has received much attention recently. Consequently, a variety of methods for this problem have been developed. Different methods employ different statistical models, and thus implicitly encode different assumptions about the nature of the underlying haplotype structure. Depending on the population sample in question, their relative performance can vary greatly, and it is unclear which method to choose for a particular sample. Instead of choosing a single method, we explore combining predictions returned by different methods in a principled way, and thereby circumvent the problem of method selection. We propose several techniques for combining haplotype reconstructions and analyze their computational properties. In an experimental study on real-world haplotype data we show that such techniques can provide more accurate and robust reconstructions, and are useful for out...

  9. Search Combinators

    CERN Document Server

    Schrijvers, Tom; Wuille, Pieter; Samulowitz, Horst; Stuckey, Peter J


    The ability to model search in a constraint solver can be an essential asset for solving combinatorial problems. However, existing infrastructure for defining search heuristics is often inadequate. Either modeling capabilities are extremely limited or users are faced with a general-purpose programming language whose features are not tailored towards writing search heuristics. As a result, major improvements in performance may remain unexplored. This article introduces search combinators, a lightweight and solver-independent method that bridges the gap between a conceptually simple modeling language for search (high-level, functional and naturally compositional) and an efficient implementation (low-level, imperative and highly non-modular). By allowing the user to define application-tailored search strategies from a small set of primitives, search combinators effectively provide a rich domain-specific language (DSL) for modeling search to the user. Remarkably, this DSL comes at a low implementation cost to the...

  10. 胎儿颈项透明层联合中孕产前无创DNA检测在胎儿染色体疾病产前筛查中的应用%Application of nuchal translu-cency in combination with non-invasive prenatal DNA test in fetal chromosomal disease

    Institute of Scientific and Technical Information of China (English)

    刘灿; 王坤; 李丽霞; 王明辉; 徐翠; 张风琴; 卢克新


    目的:探讨胎儿颈项透明层联合产前无创DNA检测在胎儿染色体疾病产前筛查中的临床应用价值.方法:2010年10月至2014年6月我院妇产科门诊就诊的孕11 ~ 14周孕妇713例,测量胎儿颈项透明层厚度,厚度异常的孕妇根据自愿行无创DNA检测,并随访观察. 结果: 713例孕妇超声检查提示胎儿颈项透明层增厚27例,21例行无创DNA检查,21-三体3例,18-三体1例,17例染色体核型正常的胎儿在以后的超声检查随访中6例出现异常. 6例未行无创DNA检查的孕妇在以后的超声检查随访中2例出现异常;21-三体胎儿的颈项透明层厚度范围为3.7 ~ 4.4 mm, 平均4.0 mm;1例18-三体胎儿的颈项透明层厚度约5.0 mm.结论:胎儿颈项透明层厚度联合无创DNA 检测能够提高胎儿染色体疾病的检出率,减少染色体异常胎儿出生率.%Objective To assess the value of nuchal translu-cency in combination with non-invasive prenatal DNA test in fetal with chromosomal disease. Methods A total of 713 cases with single pregnancies, with 11 ~ 14 gestational weeks, were enrolled in this study. We measured the thickness of nuchal translu-cency, If the thickness was abnomal, the pregnant women would receive the non-invasive prenatal DNA test on voluntary basis and were followed up. Results There were 27 cases with abnormal NT among 713 cases. Twenty-one cases received non-invasive prenatal DNA test , the test results showed that 3 cases were trisomy 21 , 1 cases was trisomy 18. Among the 17 cases with normal chromosome karyotype, 6 cases were found abnomal during the follw-up. Two cases were found abnomal among the 6 cases undergo the non-invasive prenatal DNA test.The thickness of NT, ranging from 3.7 mm to 4.4 mm, was trisomy 21, with the average of 4.0 mm, and the thickness of NT was 5.0mm and was trisomy 18. Conclusions The application of nuchal translu-cency in combination with non-invasive prenatal DNA test could improve the ability to find

  11. Specific incorporation of an artificial nucleotide opposite a mutagenic DNA adduct by a DNA polymerase. (United States)

    Wyss, Laura A; Nilforoushan, Arman; Eichenseher, Fritz; Suter, Ursina; Blatter, Nina; Marx, Andreas; Sturla, Shana J


    The ability to detect DNA modification sites at single base resolution could significantly advance studies regarding DNA adduct levels, which are extremely difficult to determine. Artificial nucleotides that are specifically incorporated opposite a modified DNA site offer a potential strategy for detection of such sites by DNA polymerase-based systems. Here we investigate the action of newly synthesized base-modified benzimidazole-derived 2'-deoxynucleoside-5'-O-triphosphates on DNA polymerases when performing translesion DNA synthesis past the pro-mutagenic DNA adduct O(6)-benzylguanine (O(6)-BnG). We found that a mutated form of KlenTaq DNA polymerase, i.e., KTqM747K, catalyzed O(6)-BnG adduct-specific processing of the artificial BenziTP in favor of the natural dNTPs. Steady-state kinetic parameters revealed that KTqM747K catalysis of BenziTP is 25-fold more efficient for template O(6)-BnG than G, and 5-fold more efficient than natural dTMP misincorporation in adduct bypass. Furthermore, the nucleotide analogue BenziTP is required for full-length product formation in O(6)-BnG bypass, as without BenziTP the polymerase stalls at the adduct site. By combining the KTqM747K polymerase and BenziTP, a first round of DNA synthesis enabled subsequent amplification of Benzi-containing DNA. These results advance the development of technologies for detecting DNA adducts.

  12. Salt-Dependent DNA-DNA Spacings in Intact Bacteriophage lambda Reflect Relative Importance of DNA Self-Repulsion and Bending Energies

    Energy Technology Data Exchange (ETDEWEB)

    X Qiu; D Rau; V Parsegian; L Fang; C Knobler; W Gelbart


    Using solution synchrotron x-ray scattering, we measure the variation of DNA-DNA d spacings in bacteriophage {lambda} with mono-, di-, and polyvalent salt concentrations, for wild-type [48.5 x 10{sup 3} base pairs (bp)] and short-genome-mutant (37.8 kbp) strains. From the decrease in d spacings with increasing salt, we deduce the relative contributions of DNA self-repulsion and bending to the energetics of packaged phage genomes. We quantify the DNA-DNA interaction energies within the intact phage by combining the measured d spacings in the capsid with measurements of osmotic pressure in DNA assemblies under the same salt conditions in bulk solution. In the commonly used Tris-Mg buffer, the DNA-DNA interaction energies inside the phage capsids are shown to be about 1 kT/bp, an order of magnitude larger than the bending energies.

  13. DNA Barcoding for Honey Biodiversity


    Alice Valentini; Christian Miquel; Pierre Taberlet


    Honey is produced by honeybees from nectar and from secretions of living plants. It reflects the honeybees’ diet and the local plant communities. Honey also shows different plant compositions in different geographical locations. We propose a new method for studying the plant diversity and the geographical origin of honey using a DNA barcoding approach that combines universal primers and massive parallel pyrosequencing. To test this method we use two commercial honeys, one from a regional orig...

  14. Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae: the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data

    Directory of Open Access Journals (Sweden)

    Pavel Stoev


    Full Text Available We demonstrate how a classical taxonomic description of a new species can be enhanced by applying new generation molecular methods, and novel computing and imaging technologies. A cave-dwelling centipede, Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae, found in a remote karst region in Knin, Croatia, is the first eukaryotic species for which, in addition to the traditional morphological description, we provide a fully sequenced transcriptome, a DNA barcode, detailed anatomical X-ray microtomography (micro-CT scans, and a movie of the living specimen to document important traits of its ex-situ behaviour. By employing micro-CT scanning in a new species for the first time, we create a high-resolution morphological and anatomical dataset that allows virtual reconstructions of the specimen and subsequent interactive manipulation to test the recently introduced ‘cybertype’ notion. In addition, the transcriptome was recorded with a total of 67,785 scaffolds, having an average length of 812 bp and N50 of 1,448 bp (see GigaDB. Subsequent annotation of 22,866 scaffolds was conducted by tracing homologs against current available databases, including Nr, SwissProt and COG. This pilot project illustrates a workflow of producing, storing, publishing and disseminating large data sets associated with a description of a new taxon. All data have been deposited in publicly accessible repositories, such as GigaScience GigaDB, NCBI, BOLD, Morphbank and Morphosource, and the respective open licenses used ensure their accessibility and re-usability.

  15. Enzyme-guided DNA Sewing Architecture. (United States)

    Song, In Hyun; Shin, Seung Won; Park, Kyung Soo; Lansac, Yves; Jang, Yun Hee; Um, Soong Ho


    With the advent of nanotechnology, a variety of nanoarchitectures with varied physicochemical properties have been designed. Owing to the unique characteristics, DNAs have been used as a functional building block for novel nanoarchitecture. In particular, a self-assembly of long DNA molecules via a piece DNA staple has been utilized to attain such constructs. However, it needs many talented prerequisites (e.g., complicated computer program) with fewer yields of products. In addition, it has many limitations to overcome: for instance, (i) thermal instability under moderate environments and (ii) restraint in size caused by the restricted length of scaffold strands. Alternatively, the enzymatic sewing linkage of short DNA blocks is simply designed into long DNA assemblies but it is more error-prone due to the undeveloped sequence data. Here, we present, for the first time, a comprehensive study for directly combining DNA structures into higher DNA sewing constructs through the 5'-end cohesive ligation of T4 enzyme. Inspired by these achievements, the synthesized DNA nanomaterials were also utilized for effective detection and real-time diagnosis of cancer-specific and cytosolic RNA markers. This generalized protocol for generic DNA sewing is expected to be useful in several DNA nanotechnology as well as any nucleic acid-related fields.

  16. DNA Origami: Folded DNA-Nanodevices That Can Direct and Interpret Cell Behavior. (United States)

    Kearney, Cathal J; Lucas, Christopher R; O'Brien, Fergal J; Castro, Carlos E


    DNA origami is a DNA-based nanotechnology that utilizes programmed combinations of short complementary oligonucleotides to fold a large single strand of DNA into precise 2D and 3D shapes. The exquisite nanoscale shape control of this inherently biocompatible material is combined with the potential to spatially address the origami structures with diverse cargoes including drugs, antibodies, nucleic acid sequences, small molecules, and inorganic particles. This programmable flexibility enables the fabrication of precise nanoscale devices that have already shown great potential for biomedical applications such as: drug delivery, biosensing, and synthetic nanopore formation. Here, the advances in the DNA-origami field since its inception several years ago are reviewed with a focus on how these DNA-nanodevices can be designed to interact with cells to direct or probe their behavior.

  17. Analgesic combinations (United States)

    Raffa, Robert B.; Pergolizzi, Joseph V.; Tallarida, Ronald J.


    When the pathophysiology of a medical condition is multi-modal, i.e., related to multiple physiological causes or mediated by multiple pathways, the optimal strategy can be to use a drug or a combination of drugs that contribute multiple mechanisms to the therapeutic endpoint. In such situations, a rational multi-modal approach can also result in the fewest adverse effects. We discuss the quantitative analysis of multi-modal action using the treatment of pain as a practical example and give examples of its application to some widely used analgesic drugs. PMID:20338825

  18. Recursive construction and error correction of DNA molecules and libraries from synthetic and natural DNA. (United States)

    Yehezkel, Tuval Ben; Linshiz, Gregory; Kaplan, Shai; Gronau, Ilan; Ravid, Sivan; Adar, Rivka; Shapiro, Ehud


    Making error-free, custom DNA assemblies from potentially faulty building blocks is a fundamental challenge in synthetic biology. Here, we show how recursion can be used to address this challenge using a recursive procedure that constructs error-free DNA molecules and their libraries from error-prone synthetic oligonucleotides and naturally existing DNA. Specifically, we describe how divide and conquer (D&C), the quintessential recursive problem-solving technique, is applied in silico to divide target DNA sequences into overlapping, albeit error prone, oligonucleotides, and how recursive construction is applied in vitro to combine them to form error-prone DNA molecules. To correct DNA sequence errors, error-free fragments of these molecules are then identified, extracted, and used as new, typically longer and more accurate, inputs to another iteration of the recursive construction procedure; the entire process repeats until an error-free target molecule is formed. The method allows combining synthetic and natural DNA fragments into error-free designer DNA libraries, thus providing a foundation for the design and construction of complex synthetic DNA assemblies.

  19. Flow cytometric detection method for DNA samples

    Energy Technology Data Exchange (ETDEWEB)

    Nasarabadi,Shanavaz (Livermore, CA); Langlois, Richard G. (Livermore, CA); Venkateswaran, Kodumudi S. (Round Rock, TX)


    Disclosed herein are two methods for rapid multiplex analysis to determine the presence and identity of target DNA sequences within a DNA sample. Both methods use reporting DNA sequences, e.g., modified conventional Taqman.RTM. probes, to combine multiplex PCR amplification with microsphere-based hybridization using flow cytometry means of detection. Real-time PCR detection can also be incorporated. The first method uses a cyanine dye, such as, Cy3.TM., as the reporter linked to the 5' end of a reporting DNA sequence. The second method positions a reporter dye, e.g., FAM.TM. on the 3' end of the reporting DNA sequence and a quencher dye, e.g., TAMRA.TM., on the 5' end.

  20. DNA computing of solutions to knapsack problems. (United States)

    Henkel, Christiaan V; Bäck, Thomas; Kok, Joost N; Rozenberg, Grzegorz; Spaink, Herman P


    One line of DNA computing research focuses on parallel search algorithms, which can be used to solve many optimization problems. DNA in solution can provide an enormous molecular library, which can be searched by molecular biological techniques. We have implemented such a parallel search for solutions to knapsack problems, which ask for the best way to pack a knapsack of limited volume. Several instances of knapsack problems were solved using DNA. We demonstrate how the computations can be extended by in vivo translation of the DNA library into protein. This combination of DNA and protein allows for multi-criterion optimization. The knapsack computations performed can then be seen as protein optimizations, one of the most complex computations performed by natural systems.

  1. DNA fingerprinting, DNA barcoding, and next generation sequencing technology in plants. (United States)

    Sucher, Nikolaus J; Hennell, James R; Carles, Maria C


    DNA fingerprinting of plants has become an invaluable tool in forensic, scientific, and industrial laboratories all over the world. PCR has become part of virtually every variation of the plethora of approaches used for DNA fingerprinting today. DNA sequencing is increasingly used either in combination with or as a replacement for traditional DNA fingerprinting techniques. A prime example is the use of short, standardized regions of the genome as taxon barcodes for biological identification of plants. Rapid advances in "next generation sequencing" (NGS) technology are driving down the cost of sequencing and bringing large-scale sequencing projects into the reach of individual investigators. We present an overview of recent publications that demonstrate the use of "NGS" technology for DNA fingerprinting and DNA barcoding applications.

  2. Radiosensitive Severe Combined Immunodeficiency Disease


    Dvorak, Christopher C.; Cowan, Morton J.


    Inherited defects in components of the non-homologous end joining DNA repair mechanism produce a T-B-NK+ severe combined immunodeficiency disease (SCID) characterized by heightened sensitivity to ionizing radiation. Patients with the radiosensitive form of SCID may also have increased short- and long-term sensitivity to the alkylator-based chemotherapy regimens traditionally utilized for conditioning prior to allogeneic hematopoietic cell transplantation (HCT). Known etiologies of radiosensit...

  3. Purification of total DNA extracted from activated sludge

    Institute of Scientific and Technical Information of China (English)


    Purification of the total DNA extracted from activated sludge samples was studied. The effects of extraction buffers and lysis treatments (lysozyme, sodium dodecyl sulfate (SDS), sonication, mechanical mill and thermal shock) on yield and purity of the total DNA extracted from activated sludge were investigated. It was found that SDS and mechanical mill were the most effective ways for cell lysis, and both gave the highest DNA yields, while by SDS and thermal shock, the purest DNA extract could be obtained. The combination of SDS with other lysis treatment, such as sonication and thermal shock, could apparently increase the DNA yields but also result in severe shearing. For the purification of the crude DNA extract, polyvinyl polypyrrolidone was used for the removal of humic contaminants. Cetyltrimethyl ammonium bromide, potassium acetate and phenol/chloroform were used to remove proteins and polysaccharides from crude DNA. Crude DNA was further purified by isopropanol precipitation. Thus, a suitable protocol was proposed for DNA extraction, yielding about 49.9 mg (DNA)/g volatile suspended solids, and the DNA extracts were successfully used in PCR amplifications for 16S rDNA and 16S rDNA V3 region. The PCR products of 16S rDNA V3 region allowed the DGGE analysis (denatured gradient gel electrophoresis) to be possible.


    Institute of Scientific and Technical Information of China (English)

    庄维城; 潘瑞彭; 欧阳仁荣; 杜心垿; 蒋莉芳; 陈小龙; 宣政华; 奚志红


    DNA differential stain is a simple method distinguishing cells of proliferative from quiescent stage. Double stranded DNA in quiescent cells is easily denatured by weak acid into single strand. As double stranded nucleic acid combined with methyl green and single stranded nucleic acid with pyronin, we make use of methyl green pyronin staining method to the cells treated with weak acid to distinguish proliferating from quiescent cells. This paper reports the observation of leukemia cells in the bone marrow smears of 100 cases of untreated acute leukemia by DNA differential staining method. The percentage of Go cells was lowest in ALL and highest in APL.

  5. 腹腔积液细胞DNA倍体及miRNA-21联合检测对肝细胞癌诊断的临床价值%Diagnostic value of combined determination of DNA ploidy level and miRNA-2 1 expression in ascites cells for hepa-tocellular carcinoma

    Institute of Scientific and Technical Information of China (English)

    肖作汉; 孟冈; 王立志; 孙文锦


    目的:评估联合检测腹腔积液细胞DNA倍体与微小RNA-21(miRNA-21)表达诊断肝细胞癌(HCC)的效能。方法将2012年1月1日-2014年1月1日鄂州市中心医院所收治临床表现伴有腹腔积液的患者纳入研究,HCC患者分入试验组,非HCC患者分入对照组。比较两组患者相关危险因素指标的差异性,采用Logistic回归分析进一步提取独立敏感指标,绘制相应指标的ROC曲线,计算曲线下面积(AUC)及约登指数(YI)。结果两组患者组间资料单因素比较显示:性别(男性比例)、吸烟史、HBV阳性、上腹部CT疑似阳性、卡氏功能量表(KPS量表)、ALT、甲胎蛋白(AFP)、异常凝血酶原(APT)、α-L-岩藻糖苷酶(AFU )、腹水细胞miRNA-21、腹水细胞DNA异倍体阳性共计11项指标差异存在统计学意义(P值均<0.05)。Logistic回归分析显示,吸烟史、AFP、APT、腹水细胞miRNA-21、腹水细胞DNA异倍体是诊断HCC的敏感指标。腹水细胞miRNA-21与DNA异倍体的AUC分别为0.742与0.801;吸烟史、AFP与APT三者联合断HCC的AUC为0.852,YI为0.5992。吸烟史、AFP、APT腹水细胞miRNA-21与DNA异倍体五项指标联合诊断的AUC增至0.869、YI增至0.6222。结论腹水细胞DNA异倍体与miRNA-21是诊断HCC的独立危险因素,单项指标检测即具有良好的诊断价值,将其联用能够显著增大HCC的诊断价值,对于该病的早期诊断具有重要临床意义,是当前HCC诊断体系的良好补充。%Objective To evaluate the diagnostic value of combined determination of DNA ploidy level and microRNA-21 (miRNA-21) expression in ascites cells for hepatocellular carcinoma (HCC).Methods A total of 1 17 patients with ascites admitted to our hospital from January 1,2012 to January 1,2014 were enrolled.The patients with a confirmed diagnosis of HCC were assigned to experimental group (n=48),and those without

  6. Karyotyping of Brassica oleracea L.based on rDNA and Cot-1 DNA fluorescence in situ hybridization

    Institute of Scientific and Technical Information of China (English)

    WANG Taixia; WU Chunhong; HUANG Jinyong; WEI Wenhui


    To explore an effective and reliable karyotyping method in Brassica crop plants,Cot-1 DNA was isolated from Brassica oleracea genome,labeled as probe with Biotin-Nick Translation Mix kit,in situ hybridized to mitotic spreads,and where specific fluorescent bands showed on each chromosome pair.25S and 5S rDNA were labeled as probes with DIG-Nick Translation Mix kit and Biotin-Nick Translation Mix kit,respectively,in situ hybridized to mitotic preparations,where 25S rDNA could be detected on two chromosome pairs and 5S rDNA on only one.Cot-1 DNA contains rDNA and chromosome sites identity between Cot-1 DNA and 25S rDNA was determined by dual-colour fluorescence in situ hybridization.All these showed that the karyotyping technique based on a combination of rDNA and Cot-1 DNA chromosome landmarks is superior to all but one.A more exact karyotype ofB.oleracea has been analyzed based on a combination of rDNA sites,Cot-1 DNA fluorescent bands,chromosome lengths and arm ratios.

  7. DNA fragmentation in apoptosis

    Institute of Scientific and Technical Information of China (English)


    Cleavage of chromosomal DNA into oligonucleosomal size fragments is an integral part of apoptosis. Elegant biochemical work identified the DNA fragmentation factor (DFF) as a major apoptotic endonuclease for DNA fragmentation in vitro. Genetic studies in mice support the importance of DFF in DNA fragmentation and possibly in apoptosis in vivo. Recent work also suggests the existence of additional endonucleases for DNA degradation. Understanding the roles of individual endonucleases in apoptosis, and how they might coordinate to degrade DNA in different tissues during normal development and homeostasis, as well as in various diseased states, will be a major research focus in the near future.

  8. ex vivo DNA assembly

    Directory of Open Access Journals (Sweden)

    Adam B Fisher


    Full Text Available Even with decreasing DNA synthesis costs there remains a need for inexpensive, rapid and reliable methods for assembling synthetic DNA into larger constructs or combinatorial libraries. Advances in cloning techniques have resulted in powerful in vitro and in vivo assembly of DNA. However, monetary and time costs have limited these approaches. Here, we report an ex vivo DNA assembly method that uses cellular lysates derived from a commonly used laboratory strain of Escherichia coli for joining double-stranded DNA with short end homologies embedded within inexpensive primers. This method concurrently shortens the time and decreases costs associated with current DNA assembly methods.

  9. Targeting DNA Repair in Cancer: Beyond PARP Inhibitors. (United States)

    Brown, Jessica S; O'Carrigan, Brent; Jackson, Stephen P; Yap, Timothy A


    Germline aberrations in critical DNA-repair and DNA damage-response (DDR) genes cause cancer predisposition, whereas various tumors harbor somatic mutations causing defective DDR/DNA repair. The concept of synthetic lethality can be exploited in such malignancies, as exemplified by approval of poly(ADP-ribose) polymerase inhibitors for treating BRCA1/2-mutated ovarian cancers. Herein, we detail how cellular DDR processes engage various proteins that sense DNA damage, initiate signaling pathways to promote cell-cycle checkpoint activation, trigger apoptosis, and coordinate DNA repair. We focus on novel therapeutic strategies targeting promising DDR targets and discuss challenges of patient selection and the development of rational drug combinations.

  10. [Uracil-DNA glycosylases]. (United States)

    Pytel, Dariusz; Słupianek, Artur; Ksiazek, Dominika; Skórski, Tomasz; Błasiak, Janusz


    Uracil is one of four nitrogen bases, most frequently found in normal RNA. Uracyl can be found also in DNA as a result of enzymatic or non-enzymatic deamination of cytosine as well as misincorporation of dUMP instead of dTMP during DNA replication. Uracil from DNA can be removed by DNA repair enzymes with apirymidine site as an intermediate. However, if uracil is not removed from DNA a pair C:G in parental DNA can be changed into a T:A pair in the daughter DNA molecule. Therefore, uracil in DNA may lead to a mutation. Uracil in DNA, similarly to thymine, forms energetically most favorable hydrogen bonds with adenine, therefore uracil does not change the coding properties of DNA. Uracil in DNA is recognized by uracil DNA glycosylase (UDGs), which initiates DNA base excision repair, leading to removing of uracil from DNA and replacing it by thymine or cytosine, when arose as a result of cytosine deamination. Eukaryotes have at least four nuclear UDGs: UNG2, SMUG1, TDG i MBD4, while UNG1 operates in the mitochondrium. UNG2 is involved in DNA repair associated with DNA replication and interacts with PCNA and RPA proteins. Uracil can also be an intermediate product in the process of antigen-dependent antibody diversification in B lymphocytes. Enzymatic deamination of viral DNA by host cells can be a defense mechanism against viral infection, including HIV-1. UNG2, MBD4 and TDG glycosylases may cooperate with mismatch repair proteins and TDG can be involved in nucleotide excision repair system.

  11. DNA damage and autophagy

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez-Rocha, Humberto; Garcia-Garcia, Aracely [Redox Biology Center and School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583 (United States); Panayiotidis, Mihalis I. [School of Community Health Sciences, University of Nevada, Reno, NV 89557 (United States); Franco, Rodrigo, E-mail: [Redox Biology Center and School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583 (United States)


    Both exogenous and endogenous agents are a threat to DNA integrity. Exogenous environmental agents such as ultraviolet (UV) and ionizing radiation, genotoxic chemicals and endogenous byproducts of metabolism including reactive oxygen species can cause alterations in DNA structure (DNA damage). Unrepaired DNA damage has been linked to a variety of human disorders including cancer and neurodegenerative disease. Thus, efficient mechanisms to detect DNA lesions, signal their presence and promote their repair have been evolved in cells. If DNA is effectively repaired, DNA damage response is inactivated and normal cell functioning resumes. In contrast, when DNA lesions cannot be removed, chronic DNA damage triggers specific cell responses such as cell death and senescence. Recently, DNA damage has been shown to induce autophagy, a cellular catabolic process that maintains a balance between synthesis, degradation, and recycling of cellular components. But the exact mechanisms by which DNA damage triggers autophagy are unclear. More importantly, the role of autophagy in the DNA damage response and cellular fate is unknown. In this review we analyze evidence that supports a role for autophagy as an integral part of the DNA damage response.

  12. cDNA-AFLP结合BSA研究马铃薯晚疫病菌小种特异无毒基因差异表达片段%Gene Expression Associated with Avirulence Gene in Phytophthora in festans Is revealed by cDNA- AFLP combined with Bulk segregant Analysis (BSA)

    Institute of Scientific and Technical Information of China (English)

    郭军; 屈冬玉; 王晓武; 金黎平; 谢开云; Rays Jiang; Francine Govers


    通过对具有6个无毒基因不同表型的马铃薯晚疫病菌构建的4个混合池进行cDNA-AFLP分析,得到与6个与无毒基因相关的差异表达片段(TDFs)85条,其中与无毒基因Avr1相关的为20条,Avr2 28条,Avr3-Avr10-Avr11 16条,Avr4 21条.差异表达片段大小主要分布在100bp和300 bp之间,最小片段为60 bp,最大片段440 bp.差异表达片段的获得将有利我们下一步克隆全长无毒基因和对晚疫病垂直抗性机制的研究.

  13. Genetic polymorphisms of 9 non-combined of DNA index system short tandem repeat loci in Guangdong Han population%九个非DNA联合索引系统核心短串联重复序列基因座在广东汉族人群的遗传多态性

    Institute of Scientific and Technical Information of China (English)

    张晋湘; 薛天羽; 李海霞; 孙宏钰; 成建定


    目的 调查D7S3048等9个非DNA联合索引系统(combined of DNA index system,CODIS)指定的核心短串联重复序列(short tandem repeat,STR)基因座在广东汉族人群的遗传多态性.方法 采用荧光标记复合扩增和毛细管电泳技术,对广东汉族500名无关个体的DNA进行9个STR基因座分型.结果 500名无关个体在D7S3048等9个非CODIS核心STR基因座共检出115个等位基因,160种基因型,各基因座杂合度为0.824~0.884,个人识别能力为0.925~0.969,多态信息总量为0.77~0.86,均符合Hardy-Weinberg平衡(P>0.05),9个STR基因座的累计个体识别力达1.00×10~(-13),三联体累计非父排除率为0.999989488,二联体累计非父排除率为0.873436.结论 D7S3048等9个STR基因座在个体识别及亲子鉴定中是一个高效的检测系统,在二联体亲子鉴定中可作为补充基因座满足疑难、单亲和突变案件的需求.%Objective To investigate the genetic polymorphisms and their forensic application of 9 non-combined of DNA index system (CODIS) short tandem repeat (STR) loci in Guangdong Han population. Methods DNA samples from 500 unrelated individuals were extracted and amplified with fluorescence labeled multiplex PCR system. PCR products were separated and genotyped with capillary electrophoresis. Results One hundred and fifteen alleles and 160 genotypes were observed in the 9 STR loci, respectively. The heterozygosity was 0. 824-0. 884, the discrimination power (DP) was 0. 925-0. 969 and the polymorphism information content (PIC) was 0. 77-0. 86, respectively. The distribution met the Hardy-Weinberg equilibrium (P>0.05). The total discrimination power was 1.00×10~(-13), the combined probability of exclusion for trio-paternity testing was 0. 999989488. The combined probability of exclusion for duo-paternity testing was 0. 873436. Conclusion The 9 STR loci are powerful and reliable for personal identification and paternity testing. They can be used as supplementary loci

  14. Combination of magnetic tweezers with DNA hairpin as a p otential approach to the study of RecA-mediated homologous recombination%磁镊结合DNA发夹的方法在RecA蛋白介导的同源重组机制研究中的潜在应用∗

    Institute of Scientific and Technical Information of China (English)

    张宇微; 颜燕; 农大官; 徐春华; 李明


    -resolution technique, the smFRET enables us to observe more details of reactions. However, its valid measuring distance is 3–8 nm, which limits the observation range. Here, we propose an approach by combining magnetic tweezers with DNA hairpin, which may solve the problem effectively in the study of HR. In this paper, one end of the DNA molecule with a 270 bp hairpin is immobilized onto the surface of the flow cell, while a magnetic bead is attached to the other end. An external magnetic force is applied to the magnetic bead by placing a permanent magnet above the flow cell. The first 90 bp (from the junction of the hairpin) of the hairpin is homologous to the ssDNA within the ssDNA-RecA filament. Thus, the filament searches for homology along the hairpin, and incorporates into the homologous segment for strand exchange. After that, the displaced strand can be opened by pulling at a force of ∼7 pN, and each opened base pair results in a 0.82 nm increase in DNA extension. By using this approach, we show that 1) RecA-mediated strand exchange proceeds in a stepwise manner and the average speed is∼7.6 nt/s, which is in accordance with previous result;2) the dynamic interaction between the second DNA-binding site (SBS) and the displaced strand can be observed in real-time, and the binding force is calculated accurately through the x-dimensional fluctuations; 3) the processes of strand-exchange in different directions can be observed, and the directions are distinguishable through the reaction patterns. The results suggest that the combination of magnetic tweezers with DNA hairpin is a potential approach to the study of RecA or other recombinases. Therefore, our design can be an important single-molecule approach to the research of HR mechanism.

  15. Sequential addition of short DNA oligos in DNA-polymerase-based synthesis reactions (United States)

    Gardner, Shea N.; Mariella, Jr., Raymond P.; Christian, Allen T.; Young, Jennifer A.; Clague, David S.


    A method of fabricating a DNA molecule of user-defined sequence. The method comprises the steps of preselecting a multiplicity of DNA sequence segments that will comprise the DNA molecule of user-defined sequence, separating the DNA sequence segments temporally, and combining the multiplicity of DNA sequence segments with at least one polymerase enzyme wherein the multiplicity of DNA sequence segments join to produce the DNA molecule of user-defined sequence. Sequence segments may be of length n, where n is an even or odd integer. In one embodiment the length of desired hybridizing overlap is specified by the user and the sequences and the protocol for combining them are guided by computational (bioinformatics) predictions. In one embodiment sequence segments are combined from multiple reading frames to span the same region of a sequence, so that multiple desired hybridizations may occur with different overlap lengths. In one embodiment starting sequence fragments are of different lengths, n, n+1, n+2, etc.

  16. Preparation of Phi29 DNA polymerase free of amplifiable DNA using ethidium monoazide, an ultraviolet-free light-emitting diode lamp and trehalose.

    Directory of Open Access Journals (Sweden)

    Hirokazu Takahashi

    Full Text Available We previously reported that multiply-primed rolling circle amplification (MRPCA using modified random RNA primers can amplify tiny amounts of circular DNA without producing any byproducts. However, contaminating DNA in recombinant Phi29 DNA polymerase adversely affects the outcome of MPRCA, especially for negative controls such as non-template controls. The amplified DNA in negative control casts doubt on the result of DNA amplification. Since Phi29 DNA polymerase has high affinity for both single-strand and double-stranded DNA, some amount of host DNA will always remain in the recombinant polymerase. Here we describe a procedure for preparing Phi29 DNA polymerase which is essentially free of amplifiable DNA. This procedure is realized by a combination of host DNA removal using appropriate salt concentrations, inactivation of amplifiable DNA using ethidium monoazide, and irradiation with visible light from a light-emitting diode lamp. Any remaining DNA, which likely exists as oligonucleotides captured by the Phi29 DNA polymerase, is degraded by the 3'-5' exonuclease activity of the polymerase itself in the presence of trehalose, used as an anti-aggregation reagent. Phi29 DNA polymerase purified by this procedure has little amplifiable DNA, resulting in reproducible amplification of at least ten copies of plasmid DNA without any byproducts and reducing reaction volume. This procedure could aid the amplification of tiny amounts DNA, thereby providing clear evidence of contamination from laboratory environments, tools and reagents.

  17. Diagnostic validity of cervical precancerous lesions by liquid-based cytology technique combined with high-risk HPV-DNA detection%液基细胞学技术联合高危HPV-DNA检测对宫颈癌前病变的诊断效度

    Institute of Scientific and Technical Information of China (English)

    王泽曼; 陈玉; 郑建鹏


    目的:探讨液基细胞学检查技术(LCT)联合高危人乳头状瘤病毒DNA(HPV-DNA)检测诊断宫颈癌前病变的效度.方法:对2007年12月~2010年12月来我院行体检的19~65岁的6 521名女性采用LCT进行宫颈癌的筛查,以及HPV分型基因芯片检测系统进行18种高危HPV基因亚型检测.对上述检测阳性者行阴道镜下宫颈活组织检查,对检测均阴性者依其意愿进行阴道镜下宫颈活组织检查.结果:LCT阳性(≥ASCUS)152例,HPV阳性86例,其中二者均为阳性的有42例,LCT和HPV均为阴性的有6 325例;LCT阳性的152例和HPV阳性的86例中病理活组织检查结果为阳性(≥CIN I)的分别有112例和68例,其中LCT和HPV均阳性的42例中病理活组织检查阳性的有34例.LCT和HPV均为阴性的6 325例中有2 000人自愿行病理检查,其中1人病理检查结果为阳性.LCT诊断宫颈癌前病变的灵敏度为76.19%,特异度为98.05%;HPV检测诊断宫颈癌前病变的灵敏度为46.26%,特异度为99.12%;两方法联合诊断(其中1项阳性即判定为患者)宫颈癌前病变的灵敏度为99.32%,特异度为99.61%.结论:液基细胞检测技术和高危HPV-DNA检测的联合应用优于单项技术检测,对于宫颈癌前病变的筛检具有重要意义.%AIM: To investigate liquid - based cytology technique ( LCT ) combined with high - risk human papilloma virus DNA ( HPV - DNA ) detection for diagnosis of cervical precancerous lesions. METHODS: Screening of cervical cancer was performed by LCT combined with HPV - DNA detection in 6 521 women at the age of 19 ~65 in our hospital for physical examination from December 2007 to December 2010. Eighteen high - risk HPV isoform genes were detected by HPV typing gene chip detection system. The women with positive detection underwent colposcopic cervical biopsies. The women with negative detection also underwent colposcopic cervical biopsies if the operation was of their own accord. RESULTS: The LCT positive results

  18. DNA packaging induced by micellar aggregates: a novel in vitro DNA condensation system. (United States)

    Ghirlando, R; Wachtel, E J; Arad, T; Minsky, A


    Evidence for a conceptually novel DNA packaging process is presented. X-ray scattering, electron microscopy, and circular dichroism measurements indicate that in the presence of positively charged micellar aggregates and flexible anionic polymers, such as negatively charged polypeptides or single-stranded RNA species, a complex is formed in which DNA molecules are partially embedded within a micellar scaffold and partially condensed into highly packed chiral structures. Based on studies of micelle-DNA and micelle-flexible anionic polymer systems, as well as on the known effects of a high charge density upon the micellar organization, a DNA packaging model is proposed. According to this model, the DNA induces the elongation of the micelles into rodlike aggregates, forming a closely packed matrix in which the DNA molecules are immobilized. In contrast, the flexible anionic polymers stabilize clusters of spherical micelles which are proposed to effect a capping of the rodlike micelles, thus arresting their elongation and creating surfactant-free segments of the DNA that are able to converge and collapse. Thus, unlike other in vitro DNA packaging systems, in which condensation follows encounters between charge-neutralized DNA molecules, a prepackaging phase where the DNA is immobilized within a matrix is proposed in this case. Cellular and nuclear membranes have been implicated in DNA packaging processes in vivo, and negatively charged polyelectrolytes were shown to be involved in the processes. These observations, combined with the basic tenets of the DNA condensation system described here, allow for the progression to the study of more elaborate model systems and thus might lead to insights into the nature and roles of the intricate in vivo DNA-membrane complexes.

  19. DNA tagged microparticles

    Energy Technology Data Exchange (ETDEWEB)

    Farquar, George Roy; Leif, Roald N; Wheeler, Elizabeth


    A simulant that includes a carrier and DNA encapsulated in the carrier. Also a method of making a simulant including the steps of providing a carrier and encapsulating DNA in the carrier to produce the simulant.

  20. Modeling DNA Replication. (United States)

    Bennett, Joan


    Recommends the use of a model of DNA made out of Velcro to help students visualize the steps of DNA replication. Includes a materials list, construction directions, and details of the demonstration using the model parts. (DDR)

  1. Click chemistry with DNA


    El-Sagheer, Afaf H.; Brown, Tom


    The advent of click chemistry has led to an influx of new ideas in the nucleic acids field. The copper catalysed alkyne–azide cycloaddition (CuAAC) reaction is the method of choice for DNA click chemistry due to its remarkable efficiency. It has been used to label oligonucleotides with fluorescent dyes, sugars, peptides and other reporter groups, to cyclise DNA, to synthesise DNA catenanes, to join oligonucleotides to PNA, and to produce analogues of DNA with modified nucleobases and backbone...

  2. 联合检测AnuA、ANA、抗ds-DNA、ENA在SLE患者中的临床应用%Clinical Application of Combined Detection of AnuA,ANA,anti ds-DNA and anti-ENA in SLE Patients

    Institute of Scientific and Technical Information of China (English)



    目的 联合检测SLE患者的多种自身抗体,为临床诊疗提供依据.方法 免疫印迹法检测120例SLE患者AnuA、抗Sm、抗SSA、抗SSB、抗Rib,间接免疫荧光法(IIF)检测抗ds-DNA和ANA,60例健康体检者做为对照组.结果 SLE患者ANA、抗ds-DNA、AunA、抗Sm、抗SSA、抗SSB和抗Rib阳性率分别为69.2%、70.8%、74.2%、35.0%、42.5%、11.7%和26.7%.活动期ANA、抗ds-DNA和AunA阳性率分别为90.7%、98.1%和83.3%,非活动期分别为51.5%、48.5%和66.7%,三项指标差异均有统计学意义(P<0.01、P<0.01和P<0.05). 60例对照组各项检测结果均为阴性.结论 联合检测SLE多种自身抗体在提高SLE的诊断分型及疗效评价等方面具有重要意义.%Objective To combine detection of SLE patients with a variety of autoantibodies, provide a basis for clinical diagnose and treat-ment. Methods AnuA,anti-Sm,anti-SSA,anti-SSB and anti-Rib were determined by western blotting,and anti-ds-DNA and ANA were determined by indirect immunofluorescence(IIF) in 120 cases of SLE patients and 60 controls. Results The positive rates of ANA,anfi ds-DNA, AunA, anti-Sm, anti-SSA, anti-SSB and anti-Rib was 69.2%, 70.8%, 74.2%, 35%, 42.5%, 11.7% and 26.7% in SLE patients. The positive rates of ANA,anti ds-DNA and AunA was 90.7%,98.1% and 83.3% in patients with active stage of SLE. The positive rates of ANA, anti ds-DNA and AunA was 51.5%,48.5% and 66.7% in patients with inactive stage of SLE. Three indicators had statistically signitieance in active stage and inactive stage(P<0.01,P< 0.01 and P< 0.05). All of the test results of 60 controls were negative. Conclusion Combined detection of several autoantibody was important to diagnosis and curative evaluation in SLE.

  3. Detection of rpoB mutations in rifampin-resistant Mycobacterium tuberculosis by use of rolling circle amplification combined with the DNA chip technology%RCA技术联合DNA芯片检测结核分枝杆菌rpoB基因突变

    Institute of Scientific and Technical Information of China (English)

    张江峰; 张亚丽; 曾照芳


    目的:应用滚环扩增(rolling circle amplification,RCA)技术以DNA芯片为载体建立一种对结核分枝杆菌耐药基因单碱基突变的快速检测方法.方法:根据结核分枝杆菌利福平耐药rpoB基因序列,设计针对该基因常见突变位点的锁式探针,及固定于基因芯片上的捕获探针.针对临床结核分枝杆菌样本的基因组DNA,PCR扩增含有rpoB基因常见突变位点的特异性DNA片段.将与突变型特异性互补结合并环化的锁式探针与芯片上固定的捕获探针进行杂交,并运用滚环扩增技术,将含有生物素标记的dUTP掺入扩增产物,最后通过与亲和素标记的纳米金反应,并银染增强显色.同时与临床样本的测序结果比较.结果:通过优化反应条件,能特异性的检测出结核分枝杆菌耐利福平rpoB基因的单碱基突变,通过对临床样本的检测,结果与测序结果一致.结论:该方法结合了DNA芯片和滚环扩增技术,能够快速有效的检测出耐药结核的单碱基突变,具有高特异性、高灵敏度.%Objective:To establish a method for rapid detection of single base mutations in resistant Myeobacterium tuberculosis by use of rolling circle amplification combined with the DNA chip technology. Methods According to rpoB gene sequence of Myeobacterium tuberculosis rifampicin resistant, padlock probes of the gene mutation types and the capture probe fixed on the gene chip were designed. Amplification of PCR containing rpoB gene mutation types of specific DNA fragments. Padlock probes via connection and cycclization, hybridization with the capture probe fixed on the gene chip. Using rolling circle amplification doped biotin labeled dUTP into the amplification product, finally through with streptavidin labeled gold nanoparticles reaction, and silver enhancement staining, compared with sequencing. Reults By optimizing the reaction conditions, specific detection of Myeobacterium tuberculosis is rifampicin resistant rpo

  4. Strategies and hurdles using DNA vaccines to fish. (United States)

    Hølvold, Linn B; Myhr, Anne I; Dalmo, Roy A


    DNA vaccinations against fish viral diseases as IHNV at commercial level in Canada against VHSV at experimental level are both success stories. DNA vaccination strategies against many other viral diseases have, however, not yet yielded sufficient results in terms of protection. There is an obvious need to combat many other viral diseases within aquaculture where inactivated vaccines fail. There are many explanations to why DNA vaccine strategies against other viral diseases fail to induce protective immune responses in fish. These obstacles include: 1) too low immunogenicity of the transgene, 2) too low expression of the transgene that is supposed to induce protection, 3) suboptimal immune responses, and 4) too high degradation rate of the delivered plasmid DNA. There are also uncertainties with regard distribution and degradation of DNA vaccines that may have implications for safety and regulatory requirements that need to be clarified. By combining plasmid DNA with different kind of adjuvants one can increase the immunogenicity of the transgene antigen - and perhaps increase the vaccine efficacy. By using molecular adjuvants with or without in combination with targeting assemblies one may expect different responses compared with naked DNA. This includes targeting of DNA vaccines to antigen presenting cells as a central factor in improving their potencies and efficacies by means of encapsulating the DNA vaccine in certain carriers systems that may increase transgene and MHC expression. This review will focus on DNA vaccine delivery, by the use of biodegradable PLGA particles as vehicles for plasmid DNA mainly in fish.

  5. Replicating animal mitochondrial DNA

    Directory of Open Access Journals (Sweden)

    Emily A. McKinney


    Full Text Available The field of mitochondrial DNA (mtDNA replication has been experiencing incredible progress in recent years, and yet little is certain about the mechanism(s used by animal cells to replicate this plasmid-like genome. The long-standing strand-displacement model of mammalian mtDNA replication (for which single-stranded DNA intermediates are a hallmark has been intensively challenged by a new set of data, which suggests that replication proceeds via coupled leading-and lagging-strand synthesis (resembling bacterial genome replication and/or via long stretches of RNA intermediates laid on the mtDNA lagging-strand (the so called RITOLS. The set of proteins required for mtDNA replication is small and includes the catalytic and accessory subunits of DNA polymerase y, the mtDNA helicase Twinkle, the mitochondrial single-stranded DNA-binding protein, and the mitochondrial RNA polymerase (which most likely functions as the mtDNA primase. Mutations in the genes coding for the first three proteins are associated with human diseases and premature aging, justifying the research interest in the genetic, biochemical and structural properties of the mtDNA replication machinery. Here we summarize these properties and discuss the current models of mtDNA replication in animal cells.

  6. Tissue distribution of DNA adducts and their persistence in blood of mice exposed to benzene.


    Li, G.; Wang, C.; Xin, W. (Weidong); Yin, S


    Chemicals combine with DNA, resulting in DNA damage, which could initiate carcinogenesis. To study whether benzene or benzene metabolites bind to DNA, DNA adducts in various tissues and their persistence in leukocytes were examined using the 32P-postlabeling assay. LACA mice were dosed ip with benzene at 500 mg/kg bw twice for 5 days. Two additional spots of DNA adducts are formed in bone marrow cells, liver cells, and peripheral blood compared with control mice. The relative adduct labeling ...

  7. Three-Dimensional DNA Nanostructures Assembled from DNA Star Motifs. (United States)

    Tian, Cheng; Zhang, Chuan


    Tile-based DNA self-assembly is a promising method in DNA nanotechnology and has produced a wide range of nanostructures by using a small set of unique DNA strands. DNA star motif, as one of DNA tiles, has been employed to assemble varieties of symmetric one-, two-, three-dimensional (1, 2, 3D) DNA nanostructures. Herein, we describe the design principles, assembly methods, and characterization methods of 3D DNA nanostructures assembled from the DNA star motifs.

  8. Methods in DNA methylation profiling. (United States)

    Zuo, Tao; Tycko, Benjamin; Liu, Ta-Ming; Lin, Juey-Jen L; Huang, Tim H-M


    Metastable and somatically heritable patterns of DNA methylation provide an important level of genomic regulation. In this article, we review methods for analyzing these genome-wide epigenetic patterns and offer a perspective on the ever-expanding literature, which we hope will be useful for investigators who are new to this area. The historical aspects that we cover will be helpful in interpreting this literature and we hope that our discussion of the newest analytical methods will stimulate future progress. We emphasize that no single approach can provide a complete view of the overall methylome, and that combinations of several modalities applied to the same sample set will give the clearest picture. Given the unexpected epigenomic patterns and new biological principles, as well as new disease markers, that have been uncovered in recent studies, it is likely that important discoveries will continue to be made using genome-wide DNA methylation profiling.

  9. Radiosensitive Severe Combined Immunodeficiency Disease (United States)

    Dvorak, Christopher C.; Cowan, Morton J.


    Synopsis Inherited defects in components of the non-homologous end joining DNA repair mechanism produce a T-B-NK+ severe combined immunodeficiency disease (SCID) characterized by heightened sensitivity to ionizing radiation. Patients with the radiosensitive form of SCID may also have increased short- and long-term sensitivity to the alkylator-based chemotherapy regimens traditionally utilized for conditioning prior to allogeneic hematopoietic cell transplantation (HCT). Known etiologies of radiosensitive SCID include deficiencies of Artemis, DNA Ligase IV, DNA-dependent protein kinase catalytic subunit (DNA-PKcs), and Cernunnos-XLF, all of which have been treated with HCT. Because of their sensitivity to certain forms of chemotherapy, the approach to donor selection and type of conditioning regimen utilized for a radiosensitive SCID patient requires careful consideration. Significantly more research needs to be done in order to determine the long-term outcomes of radiosensitive SCID patients following HCT, as well as to discover novel non-toxic approaches to HCT that might benefit those with intrinsic radio- and chemo-sensitivity, as well as potentially all patients undergoing an HCT. PMID:20113890

  10. Value of Detecting Peripheral Blood Cell Morphology Combined with EBV-DNA Quantity in the Initial Diagnosis for Infants Patients with Infectious Mononucleosis%外周血细胞形态学检查与EBV-DNA定量分析在小儿传染性单核细胞增多症早期诊断中的价值

    Institute of Scientific and Technical Information of China (English)

    肖波; 毛金娥; 陈万新


    quantity were both detected in the initial fever period and a week later.The latter was detected by real-time quantitative PCR (RT-qPCR),combined with all the symptoms were all analysed comprehensively.The percentage of abnormal lymphocyte more than 10% was positive,and the EBV-DNA quantity more than 1.0×103 copy per ml was posi-tive,too.Results Of all the infants patients,in the initial fever period,82 patients had more than 10% positive abnormal lymphocyte and 100 patients had positive EBV-DNA quantity.But a week later,156 patients had more than 10% positive ab-normal lymphocyte,the maximum abnormal lymphocyte was 56%.And 180 patients had positive EBV-DNA quantity.When both abnormal lymphocyte morphology in peripheral blood and Epstein Barr Virus (EBV)DNA quantity were detected,in the initial fever period,125 patients were positive,it rose significantly more than that of abnormal lymphocyte morphology in peripheral blood (χ2=17.45,P0.05).Conclusion The detecting of peripheral blood cell morphology combined with EBV-DNA quantity are very important in the initial diagnosis for infants patients with infectious mononucleosis.Including all the symp-toms,they could improve the diagnosis timely and accurately.

  11. DNA Origami Reorganizes upon Interaction with Graphite: Implications for High-Resolution DNA Directed Protein Patterning

    Directory of Open Access Journals (Sweden)

    Masudur Rahman


    Full Text Available Although there is a long history of the study of the interaction of DNA with carbon surfaces, limited information exists regarding the interaction of complex DNA-based nanostructures with the important material graphite, which is closely related to graphene. In view of the capacity of DNA to direct the assembly of proteins and optical and electronic nanoparticles, the potential for combining DNA-based materials with graphite, which is an ultra-flat, conductive carbon substrate, requires evaluation. A series of imaging studies utilizing Atomic Force Microscopy has been applied in order to provide a unified picture of this important interaction of structured DNA and graphite. For the test structure examined, we observe a rapid destabilization of the complex DNA origami structure, consistent with a strong interaction of single-stranded DNA with the carbon surface. This destabilizing interaction can be obscured by an intentional or unintentional primary intervening layer of single-stranded DNA. Because the interaction of origami with graphite is not completely dissociative, and because the frustrated, expanded structure is relatively stable over time in solution, it is demonstrated that organized structures of pairs of the model protein streptavidin can be produced on carbon surfaces using DNA origami as the directing material.

  12. Fast phylogenetic DNA barcoding

    DEFF Research Database (Denmark)

    Terkelsen, Kasper Munch; Boomsma, Wouter Krogh; Willerslev, Eske


    We present a heuristic approach to the DNA assignment problem based on phylogenetic inferences using constrained neighbour joining and non-parametric bootstrapping. We show that this method performs as well as the more computationally intensive full Bayesian approach in an analysis of 500 insect...... DNA sequences obtained from GenBank. We also analyse a previously published dataset of environmental DNA sequences from soil from New Zealand and Siberia, and use these data to illustrate the fact that statistical approaches to the DNA assignment problem allow for more appropriate criteria...... for determining the taxonomic level at which a particular DNA sequence can be assigned....

  13. DNA: Structure and function

    DEFF Research Database (Denmark)

    Sinden, Richard R.; E. Pearson, Christopher; N. Potaman, Vladimir


    This chapter discusses the structure and function of DNA. DNA occupies a critical role in cells, because it is the source of all intrinsic genetic information. Chemically, DNA is a very stable molecule, a characteristic important for a macromolecule that may have to persist in an intact form...... for a long period of time before its information is accessed by the cell. Although DNA plays a critical role as an informational storage molecule, it is by no means as unexciting as a computer tape or disk drive. The structure of the DNA described by Watson and Crick in 1953 is a right handed helix of two...

  14. Archaeal DNA replication. (United States)

    Kelman, Lori M; Kelman, Zvi


    DNA replication is essential for all life forms. Although the process is fundamentally conserved in the three domains of life, bioinformatic, biochemical, structural, and genetic studies have demonstrated that the process and the proteins involved in archaeal DNA replication are more similar to those in eukaryal DNA replication than in bacterial DNA replication, but have some archaeal-specific features. The archaeal replication system, however, is not monolithic, and there are some differences in the replication process between different species. In this review, the current knowledge of the mechanisms governing DNA replication in Archaea is summarized. The general features of the replication process as well as some of the differences are discussed.

  15. Racemic DNA crystallography. (United States)

    Mandal, Pradeep K; Collie, Gavin W; Kauffmann, Brice; Huc, Ivan


    Racemates increase the chances of crystallization by allowing molecular contacts to be formed in a greater number of ways. With the advent of protein synthesis, the production of protein racemates and racemic-protein crystallography are now possible. Curiously, racemic DNA crystallography had not been investigated despite the commercial availability of L- and D-deoxyribo-oligonucleotides. Here, we report a study into racemic DNA crystallography showing the strong propensity of racemic DNA mixtures to form racemic crystals. We describe racemic crystal structures of various DNA sequences and folded conformations, including duplexes, quadruplexes, and a four-way junction, showing that the advantages of racemic crystallography should extend to DNA.

  16. Diagnostic Value Analysis about Anti-dsDNA Antibody, Anti-Smith Antibody and Anti-Rib-P Antibody of Systemic Lupus Erythematosus by Protein Chip Technology Combined Detection%蛋白芯片技术联合检测抗dsDNA抗体、抗Smith抗体和抗Rib-P抗体对SLE诊断价值分析

    Institute of Scientific and Technical Information of China (English)

    杨艳丽; 任健康; 李亚娥; 胡淑玲


    Objective To evaluate the combined detection of the anti-dsDNA antibody .anti-Smith antibody and anti-Rib-P antibody in protein chip technique for the diagnosis of systemic lupus erythematosus (SLE). Methods Detected the anti-ds DNA antibody.anti-Smith antibody and anti-Rib-P antibody in the serum of 85 SLE patients,129 patients with other autoimmune diseases and 43 healthy subjects by applying protein-chip technology. Results The positive rate(50. 59% ,32. 94% and 37. 65%) of anti-dsDNA antibody,anti-Smith antibody and anti-Rib-P antibody in SLE patients' serum and the positive rate (78. 82%) of their combined detection was significantly higher than that of the disease control group. There was difference (χ2:100. 269,52. 36,62.481 and 155. 51, P<0. 01). The normal control group was all negative. Among SLE patients,for the anti-dsDNA antibody,the sensitivity was 50. 59% and specificity was 99. 22%,for the anti-Smith antibody, the sensitivity was 32. 94% and specificity was 97. 67%;for the anti-Rib-P antibody, the sensitivity was 37.65% and specificity was 97. 67% ;for the three autoantibodies' combined detection, the sensitivity was 78. 82% and specificity was 94. 57%. The sensitivity of combined detection was significantly higher than that of every single detection. Conclusion As the important SLE antibodies,anti-dsDNA antibody, anti-Smith antibody and anti-Rib-P antibody with high specificity can complement with each other in the simultaneous detection on a protein chip. It improve the sensitivity and efficiency of SLE diagnosis, reduce the missed diagnosis and misdiagnosis of SLE diagnosis, so it is important for SLE diagnosis,treatment and prognosis.%目的 评价蛋白芯片技术联合检测抗dsDNA抗体、抗Smith抗体和抗Rib-P抗体对于系统性红斑狼疮(SLE)诊断的价值.方法 采用蛋白芯片技术对85例SLE患者、129例其他自身免疫性疾病患者和43例健康体检者血清中的抗dsDNA抗体、抗Smith抗体和

  17. DNA barcoding for plants. (United States)

    de Vere, Natasha; Rich, Tim C G; Trinder, Sarah A; Long, Charlotte


    DNA barcoding uses specific regions of DNA in order to identify species. Initiatives are taking place around the world to generate DNA barcodes for all groups of living organisms and to make these data publically available in order to help understand, conserve, and utilize the world's biodiversity. For land plants the core DNA barcode markers are two sections of coding regions within the chloroplast, part of the genes, rbcL and matK. In order to create high quality databases, each plant that is DNA barcoded needs to have a herbarium voucher that accompanies the rbcL and matK DNA sequences. The quality of the DNA sequences, the primers used, and trace files should also be accessible to users of the data. Multiple individuals should be DNA barcoded for each species in order to check for errors and allow for intraspecific variation. The world's herbaria provide a rich resource of already preserved and identified material and these can be used for DNA barcoding as well as by collecting fresh samples from the wild. These protocols describe the whole DNA barcoding process, from the collection of plant material from the wild or from the herbarium, how to extract and amplify the DNA, and how to check the quality of the data after sequencing.

  18. The application of HPV-DNA detection combined with VIA test in screening of precancerous lesion of uterine cervix%高危型HPV检测联合肉眼醋酸试验在宫颈癌前病变筛查中的应用

    Institute of Scientific and Technical Information of China (English)



    目的:研究在宫颈癌前病变筛查中采用高危型HPV检测联合肉眼醋酸试验的应用效果.方法:选取2007年8月~2010年2月于我院治疗的可疑宫颈癌前病变患者532例,应用5%醋酸和Lugol's 液涂抹于宫颈表面,筛选出有异常着色的患者320例,再采用实时荧光定量PCR技术检测高危型HPV病毒感染情况.结果:320例肉眼醋酸试验异常着色患者进行高危型HPV病毒感染检测发现,HPV阳性感染190例,阳性率为59.38%;212例肉眼醋酸试验正常着色患者进行高危型HPV病毒感染检测发现,HPV阳性感染18例,阳性率为8.49%.结论:肉眼醋酸试验联合高危型HPV检测可及时、有效地发现宫颈癌前病变,可作为宫颈癌前病变筛查方案应用于临床.%Objective: To study the efficiency of HPV-DNA detection combined with visual inspection with acetic acid (VIA) test in screening of precancerous lesions of uterine cervix. Methods: 532 suspected precancerous lesion of uterine cervix patients in our hospital from August 2007 to February 2010 were selected. 5% acetic acid and Lugol's liquid were painted on the surface of cervix of all patients, and 320 cases of patients were screened by the abnormal color. Then the re -al-time fluorescence quantitative polymerase chain reaction technology was used to test high risk HPV infection in all pa -tients. Results: High risk HPV infection test of 320 patients who were showed abnormal color in VIA test was showed that 190 cases got HPV positive infection, the positive rate was 59.38%. High risk HPV infection test of 212 patients who were showed normal color in VIA test was showed that 18 cases got HPV positive infection, the positive rate was 8.49%. Conclusion: VIA test combined with HPV-DNA checking can timely and effectively discover precancerous lesion, which can be used in clinic as precancerous lesion screening plan.

  19. Application of optical tweezers using DOE and SLM to control of beads with information-DNA for photonic DNA computing (United States)

    Zheng, M. J.; Ogura, Y.; Tanida, J.


    We have proposed photonic DNA computing as a new parallel computing paradigm, in which optical techniques are used to manipulate information-coded DNA. In this paper, we present a parallel transportation of multiple beads bound with hairpin-structure DNA using a dynamic optical tweezers system which combines a spatial light modulator (SLM) with a diffractive optical element (DOE). This system provides and effective method for parallel manipulations of DNA-bound beads at multiple positions. In the experiments, three 2.8-μm-diameter beads bound with hairpin DNA were trapped and transported in 1 μm of step by switching of the SLM patterns. The results demonstrate that the dynamic holographic optical tweezers system with combination of the DOE and the SLM is useful in spatially parallel processing required for photonic DNA computing.

  20. Biometric Authentication Using ElGamal Cryptosystem And DNA Sequence

    Directory of Open Access Journals (Sweden)



    Full Text Available Biometrics are automated methods of identifying a person or verifying the identity of a person based on a Physiological or behavioral characteristic. Physiological haracteristics include hand or finger images, facial characteristics and iris recognition. Behavioral characteristics include dynamic signature verification, speaker verification and keystroke dynamics. DNA is unique feature among individuals. DNA provides high security level, long term stability, user acceptance and is intrusive. Combining ElGamal cryptosystem and DNA sequence, a novel biometric authentication scheme is proposed.

  1. DNA from keratinous tissue

    DEFF Research Database (Denmark)

    Olsen, Maia E.; Bengtsson, Camilla Friis; Bertelsen, Mads Frost


    Although good quality DNA can be recovered from the base of the calamus of freshly sampled feathers, as from other fully keratinized tissues such as nail or hair shaft, the quality and quantity of DNA in the majority of feather structures is much poorer. Little research has been performed...... to characterize the quality of this DNA is, and thus what a researcher might be able to achieve when using feathers as a source of DNA. In this review, we expand on our companion article detailing the quality of DNA in nail and hair, by synthesizing published, and new preliminary genetic data obtained from...... feathers. As with nail and hair, we demonstrate that although DNA can, in general, be recovered from all parts of the feather, the quality of such DNA varies. As such, although one can expect a priori that genetic analyses are possible on the feather, for PCR based analyses, it is extremely difficult...

  2. Biophysics of DNA

    CERN Document Server

    Vologodskii, Alexander


    Surveying the last sixty years of research, this book describes the physical properties of DNA in the context of its biological functioning. It is designed to enable both students and researchers of molecular biology, biochemistry and physics to better understand the biophysics of DNA, addressing key questions and facilitating further research. The chapters integrate theoretical and experimental approaches, emphasising throughout the importance of a quantitative knowledge of physical properties in building and analysing models of DNA functioning. For example, the book shows how the relationship between DNA mechanical properties and the sequence specificity of DNA-protein binding can be analyzed quantitatively by using our current knowledge of the physical and structural properties of DNA. Theoretical models and experimental methods in the field are critically considered to enable the reader to engage effectively with the current scientific literature on the physical properties of DNA.

  3. The short-term therapeutic effects of DNA immunoadsorbent combined with medication on patients with ;severe systemic lupus erythematosus%DNA免疫吸附联合药物治疗重度系统性红斑狼疮的近期疗效观察

    Institute of Scientific and Technical Information of China (English)

    吴潮清; 黄玲; 唐业莹; 熊礼佳; 贺红光; 刘芸芳; 李瑾瑜; 王浩宇; 唐盛; 叶琨; 彭小梅


    Objective To evaluate the short-term therapeutic effects of DNA immunoadsorbent (IA) combined with glucocorticoid and immune depressant on patients with severe systemic lupus erythematosus(SLE). Methods 32 patients with severe SLE were selected to undergo DNA IA treatment combined with glucocorticoid plus cyclophosphamide therapy, and each patient received IA therapy 3 times, once 2.5 hours, with an interval of 24-48 hours to take another two times of IA. The changes in SLE disease activity index(SLEDAI)score, health status evaluation indexes〔 physiologic functional( PF) and emotional health( MH) scores〕,renal function indexes〔 blood urea nitrogen(BUN)and serum creatinine(SCr)〕 were observed; and anti-double stranded DNA antibody( ds-DNA), immunoglobulin (IgA, IgG, IgM), complements(C3 and C4)and high-sensitivity C-reactive protein (hs-CRP) were examined before and after IA treatment for 2 weeks. Results Two weeks after the combination therapy, the SLEDAI score, BUN, SCr, dsDNA, IgA, IgG, IgM, hs-CRP were significantly lower than those before treatment 〔SLEDAI score : 14.38±3.85 vs. 15.69±1.40, BUN (mmol/L): 11.22±4.78 vs. 16.31±7.90, SCr (μmol/L): 127.02±38.17 vs. 167.25±45.63, dsDNA( U/L): 1.36±0.12 vs. 1.43±0.18, IgA( g/L): 2.41±0.73 vs. 2.59±0.86, IgG( g/L): 16.82±4.83 vs. 21.01±4.84, IgM( g/L): 1.64±0.45 vs. 1.75±0.58, hs-CRP( mg/L): 14.41±2.20 vs. 14.94±2.60, P<0.05 or P<0.01〕; PF score, MH score, complement C3 were increased〔 PF score : 71.19±17.53 vs. 56.66±22.41, MH score : 74.01±15.72 vs. 61.50±17.98, C3( g/L): 0.56±0.09 vs. 0.52±0.10, all P<0.05〕; clinical symptoms were improved significantly, and no significant adverse reactions were found. Conclusion IA combined with medical treatment has shown that it has significant therapeutic effect for treatment of patients with severe SLE, and it may decrease the levels of dsDNA, IgA, IgG, IgM,hs-CRP, and increase the level of complement C3.%目的:观察DNA免疫吸附

  4. [DNA methylation and epigenetics]. (United States)

    Vaniushin, B F


    In eukaryotic cells, nuclear DNA is subject to enzymatic methylation with the formation of 5-methylcytosine residues, mostly within the CG and CNG sequences. In plants and animals this DNA methylation is species-, tissue-, and organelle-specific. It changes (decreases) with age and is regulated by hormones. On the other hand, genome methylation can control hormonal signal. Replicative and post-replicative DNA methylation types are distinguished. They are mediated by multiple DNA methyltransferases with different site-specificity. Replication is accompanied by the appearance of hemimethylated DNA sites. Pronounced asymmetry of the DNA strand methylation disappears to the end of the cell cycle. A model of methylation-regulated DNA replication is proposed. DNA methylation controls all genetic processes in the cell (replication, transcription, DNA repair, recombination, and gene transposition). It is the mechanism of cell differentiation, gene discrimination and silencing. In animals, suppression of DNA methylation stops development (embryogenesis), switches on apoptosis, and is usually lethal. Disruption of DNA methylation pattern results in the malignant cell transformation and serves as one of the early diagnostic features of carcinogenesis. In malignant cell the pattern of DNA methylation, as well as the set of DNA methyltransferase activities, differs from that in normal cell. In plants inhibition of DNA methylation is accompanied by the induction of seed storage and florescence genes. In eukaryotes one and the same gene can be simultaneously methylated both at cytosine and adenine residues. It can be thus suggested, that the plant cell contains at least two different, and probably, interdependent systems of DNA methylation. The first eukaryotic adenine DNA methyltransferase was isolated from plants. This enzyme methylates DNA with the formation of N6-methyladenine residues in the sequence TGATCA (TGATCA-->TGm6ATCA). Plants possess AdoMet-dependent endonucleases

  5. Novel DNA probes for sensitive DNA detection


    Richardson, James Alistair


    The ability to detect and interrogate DNA sequences allows further understanding and\\ud diagnosis of genetic disease. The ability to perform such analysis of genetic material\\ud requires highly selective and reliable technologies. Furthermore techniques which can use\\ud simple and cheap equipment allow the use of such technologies for point of care analysis.\\ud \\ud Described in this thesis are two novel DNA probe systems designed for mutation\\ud discrimination and sequence recognition of PCR ...

  6. Improving DNA vaccine performance through vector design. (United States)

    Williams, James A


    DNA vaccines are a rapidly deployed next generation vaccination platform for treatment of human and animal disease. DNA delivery devices, such as electroporation and needle free jet injectors, are used to increase gene transfer. This results in higher antigen expression which correlates with improved humoral and cellular immunity in humans and animals. This review highlights recent vector and transgene design innovations that improve DNA vaccine performance. These new vectors improve antigen expression, increase plasmid manufacturing yield and quality in bioreactors, and eliminate antibiotic selection and other potential safety issues. A flowchart for designing synthetic antigen transgenes, combining antigen targeting, codon-optimization and bioinformatics, is presented. Application of improved vectors, of antibiotic free plasmid production, and cost effective manufacturing technologies will be critical to ensure safety, efficacy, and economically viable manufacturing of DNA vaccines currently under development for infectious disease, cancer, autoimmunity, immunotolerance and allergy indications.

  7. Conventional and nanotechniques for DNA methylation profiling. (United States)

    Shanmuganathan, Rajasree; Basheer, Nazeema B; Amirthalingam, Laxmi; Muthukumar, Harshiny; Kaliaperumal, Rajendran; Shanmugam, Kumaran


    DNA methylation is critical for gene silencing and is associated with the incidence of many diseases, including cancer. Underlying molecular mechanisms of human diseases and tissue-specific gene expression have been elucidated based on DNA methylation studies. This review highlights the advantages and drawbacks of various methylation screening techniques: blotting, genomic sequencing, bisulfite sequencing, methylation-specific PCR, methylated DNA immunoprecipitation, microarray analysis, matrix-assisted laser desorption ionization time-of-flight mass spectroscopy, nanowire transistor detection procedure, quantum dot-based nanoassay, single-molecule real-time detection, fluorimetric assay, electrochemical detection, and atomic force spectroscopy. The review provides insight for selecting a method or a combination of methods for DNA methylation analysis. Convergence of conventional and contemporary nanotechniques to enumerate methylation at specific CpG sites of oncogene would fill the gap in diagnosis of cancer.

  8. Nanopore DNA sequencing using kinetic proofreading (United States)

    Ling, Xinsheng

    We propose a method of DNA sequencing by combining the physical method of nanopore electrical measurements and Southern's sequencing-by-hybridization. The new key ingredient, essential to both lowering the costs and increasing the precision, is an asymmetric nanopore sandwich device capable of measuring the DNA hybridization probe twice separated by a designed waiting time. Those incorrect probes appearing only once in nanopore ionic current traces are discriminated from the correct ones that appear twice. This method of discrimination is similar to the principle of kinetic proofreading proposed by Hopfield and Ninio in gene transcription and translation processes. An error analysis is of this nanopore kinetic proofreading (nKP) technique for DNA sequencing is carried out in comparison with the most precise 3' dideoxy termination method developed by Sanger. Nanopore DNA sequencing using kinetic proofreading.

  9. Targeting DNA Replication Stress for Cancer Therapy

    Directory of Open Access Journals (Sweden)

    Jun Zhang


    Full Text Available The human cellular genome is under constant stress from extrinsic and intrinsic factors, which can lead to DNA damage and defective replication. In normal cells, DNA damage response (DDR mediated by various checkpoints will either activate the DNA repair system or induce cellular apoptosis/senescence, therefore maintaining overall genomic integrity. Cancer cells, however, due to constitutive growth signaling and defective DDR, may exhibit “replication stress” —a phenomenon unique to cancer cells that is described as the perturbation of error-free DNA replication and slow-down of DNA synthesis. Although replication stress has been proven to induce genomic instability and tumorigenesis, recent studies have counterintuitively shown that enhancing replicative stress through further loosening of the remaining checkpoints in cancer cells to induce their catastrophic failure of proliferation may provide an alternative therapeutic approach. In this review, we discuss the rationale to enhance replicative stress in cancer cells, past approaches using traditional radiation and chemotherapy, and emerging approaches targeting the signaling cascades induced by DNA damage. We also summarize current clinical trials exploring these strategies and propose future research directions including the use of combination therapies, and the identification of potential new targets and biomarkers to track and predict treatment responses to targeting DNA replication stress.

  10. DNA hydration studied by neutron fiber diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Fuller, W.; Forsyth, V.T.; Mahendrasingam, A.; Langan, P.; Pigram, W.J. [Keele Univ. (United Kingdom)] [and others


    The development of neutron high angle fiber diffraction to investigate the location of water around the deoxyribonucleic acid (DNA) double-helix is described. The power of the technique is illustrated by its application to the D and A conformations of DNA using the single crystal diffractometer, D19, at the Institute Laue-Langevin, Grenoble and the time of flight diffractometer, SXD, at the Rutherford Appleton ISIS Spallation Neutron Source. These studies show the existence of bound water closely associated with the DNA. The patterns of hydration in these two DNA conformations are quite distinct and are compared to those observed in X-ray single crystal studies of two-stranded oligodeoxynucleotides. Information on the location of water around the DNA double-helix from the neutron fiber diffraction studies is combined with that on the location of alkali metal cations from complementary X-ray high angle fiber diffraction studies at the Daresbury Laboratory SRS using synchrotron radiation. These analyses emphasize the importance of viewing DNA, water and ions as a single system with specific interactions between the three components and provide a basis for understanding the effect of changes in the concentration of water and ions in inducing conformations] transitions in the DNA double-helix.

  11. DNA ligase IV syndrome; a review. (United States)

    Altmann, Thomas; Gennery, Andrew R


    DNA ligase IV deficiency is a rare primary immunodeficiency, LIG4 syndrome, often associated with other systemic features. DNA ligase IV is part of the non-homologous end joining mechanism, required to repair DNA double stranded breaks. Ubiquitously expressed, it is required to prevent mutagenesis and apoptosis, which can result from DNA double strand breakage caused by intracellular events such as DNA replication and meiosis or extracellular events including damage by reactive oxygen species and ionising radiation.Within developing lymphocytes, DNA ligase IV is required to repair programmed DNA double stranded breaks induced during lymphocyte receptor development.Patients with hypomorphic mutations in LIG4 present with a range of phenotypes, from normal to severe combined immunodeficiency. All, however, manifest sensitivity to ionising radiation. Commonly associated features include primordial growth failure with severe microcephaly and a spectrum of learning difficulties, marrow hypoplasia and a predisposition to lymphoid malignancy. Diagnostic investigations include immunophenotyping, and testing for radiosensitivity. Some patients present with microcephaly as a predominant feature, but seemingly normal immunity. Treatment is mainly supportive, although haematopoietic stem cell transplantation has been used in a few cases.

  12. Targeting DNA Replication Stress for Cancer Therapy (United States)

    Zhang, Jun; Dai, Qun; Park, Dongkyoo; Deng, Xingming


    The human cellular genome is under constant stress from extrinsic and intrinsic factors, which can lead to DNA damage and defective replication. In normal cells, DNA damage response (DDR) mediated by various checkpoints will either activate the DNA repair system or induce cellular apoptosis/senescence, therefore maintaining overall genomic integrity. Cancer cells, however, due to constitutive growth signaling and defective DDR, may exhibit “replication stress” —a phenomenon unique to cancer cells that is described as the perturbation of error-free DNA replication and slow-down of DNA synthesis. Although replication stress has been proven to induce genomic instability and tumorigenesis, recent studies have counterintuitively shown that enhancing replicative stress through further loosening of the remaining checkpoints in cancer cells to induce their catastrophic failure of proliferation may provide an alternative therapeutic approach. In this review, we discuss the rationale to enhance replicative stress in cancer cells, past approaches using traditional radiation and chemotherapy, and emerging approaches targeting the signaling cascades induced by DNA damage. We also summarize current clinical trials exploring these strategies and propose future research directions including the use of combination therapies, and the identification of potential new targets and biomarkers to track and predict treatment responses to targeting DNA replication stress. PMID:27548226

  13. Charting the Structure and Energetics of Packaged DNA in Bacteriophages (United States)

    Qiu, Xiangyun; Rau, Donald C.; Parsegian, V. Adrian; Fang, Li Tai; Knobler, Charles M.; Gelbart, William M.


    Many bacterial viruses resort to pressure in order to infect bacteria, e.g., lambda phage stores its dsDNA genome at surprisingly high pressure and then uses this pressure to drive delivery of the genome. We report on a biophysical interrogation of the DNA configuration and pressure in lambda phage by combining structural and thermodynamic measurements with theoretical modeling. Changes in DNA organization in the capsid are monitored using solution small angle x-ray scattering (SAXS). We vary the DNA-DNA repulsion and DNA bending contributions to the capsid pressure by changing salt concentrations and packaged length, and augment SAXS data with osmotic stress measurements to elicit the evolving structure and energetics of the packaged DNA.

  14. Statistical assignment of DNA sequences using Bayesian phylogenetics

    DEFF Research Database (Denmark)

    Terkelsen, Kasper Munch; Boomsma, Wouter Krogh; Huelsenbeck, John P.;


    -analysis of previously published ancient DNA data and show that, with high statistical confidence, most of the published sequences are in fact of Neanderthal origin. However, there are several cases of chimeric sequences that are comprised of a combination of both Neanderthal and modern human DNA....

  15. PNA Directed Sequence Addressed Self-Assembly of DNA Nanostructures

    DEFF Research Database (Denmark)

    Nielsen, Peter E.


    sequence specifically recognize another PNA oligomer. We describe how such three domain PNAs have utility for assembling dsDNA grid and clover leaf structures, and in combination with SNAP-tag technol. of protein dsDNA structures. (c) 2008 American Institute of Physics. [on SciFinder (R)] Udgivelsesdato...

  16. Polymorphic microsatellite DNA markers in the penduline tit, Remiz pendulinus

    NARCIS (Netherlands)

    Meszaros, L. A.; Frauenfelder, N.; Van Der Velde, M.; Komdeur, J.; Szabad, J.


    To describe the exceptional mating system of the penduline tit, Remiz pendulinus, we aim to combine field observation records with DNA analysis based on polymorphic microsatellite DNA markers. Here we describe features of nine loci and their corresponding polymerase chain reaction primers. The obser

  17. Immunization with a Vaccine Combining Herpes Simplex Virus 2 (HSV-2) Glycoprotein C (gC) and gD Subunits Improves the Protection of Dorsal Root Ganglia in Mice and Reduces the Frequency of Recurrent Vaginal Shedding of HSV-2 DNA in Guinea Pigs Compared to Immunization with gD Alone ▿ (United States)

    Awasthi, Sita; Lubinski, John M.; Shaw, Carolyn E.; Barrett, Shana M.; Cai, Michael; Wang, Fushan; Betts, Michael; Kingsley, Susan; DiStefano, Daniel J.; Balliet, John W.; Flynn, Jessica A.; Casimiro, Danilo R.; Bryan, Janine T.; Friedman, Harvey M.


    Attempts to develop a vaccine to prevent genital herpes simplex virus 2 (HSV-2) disease have been only marginally successful, suggesting that novel strategies are needed. Immunization with HSV-2 glycoprotein C (gC-2) and gD-2 was evaluated in mice and guinea pigs to determine whether adding gC-2 to a gD-2 subunit vaccine would improve protection by producing antibodies that block gC-2 immune evasion from complement. Antibodies produced by gC-2 immunization blocked the interaction between gC-2 and complement C3b, and passive transfer of gC-2 antibody protected complement-intact mice but not C3 knockout mice against HSV-2 challenge, indicating that gC-2 antibody is effective, at least in part, because it prevents HSV-2 evasion from complement. Immunization with gC-2 also produced neutralizing antibodies that were active in the absence of complement; however, the neutralizing titers were higher when complement was present, with the highest titers in animals immunized with both antigens. Animals immunized with the gC-2-plus-gD-2 combination had robust CD4+ T-cell responses to each immunogen. Multiple disease parameters were evaluated in mice and guinea pigs immunized with gC-2 alone, gD-2 alone, or both antigens. In general, gD-2 outperformed gC-2; however, the gC-2-plus-gD-2 combination outperformed gD-2 alone, particularly in protecting dorsal root ganglia in mice and reducing recurrent vaginal shedding of HSV-2 DNA in guinea pigs. Therefore, the gC-2 subunit antigen enhances a gD-2 subunit vaccine by stimulating a CD4+ T-cell response, by producing neutralizing antibodies that are effective in the absence and presence of complement, and by blocking immune evasion domains that inhibit complement activation. PMID:21813597

  18. Immunization with a vaccine combining herpes simplex virus 2 (HSV-2) glycoprotein C (gC) and gD subunits improves the protection of dorsal root ganglia in mice and reduces the frequency of recurrent vaginal shedding of HSV-2 DNA in guinea pigs compared to immunization with gD alone. (United States)

    Awasthi, Sita; Lubinski, John M; Shaw, Carolyn E; Barrett, Shana M; Cai, Michael; Wang, Fushan; Betts, Michael; Kingsley, Susan; Distefano, Daniel J; Balliet, John W; Flynn, Jessica A; Casimiro, Danilo R; Bryan, Janine T; Friedman, Harvey M


    Attempts to develop a vaccine to prevent genital herpes simplex virus 2 (HSV-2) disease have been only marginally successful, suggesting that novel strategies are needed. Immunization with HSV-2 glycoprotein C (gC-2) and gD-2 was evaluated in mice and guinea pigs to determine whether adding gC-2 to a gD-2 subunit vaccine would improve protection by producing antibodies that block gC-2 immune evasion from complement. Antibodies produced by gC-2 immunization blocked the interaction between gC-2 and complement C3b, and passive transfer of gC-2 antibody protected complement-intact mice but not C3 knockout mice against HSV-2 challenge, indicating that gC-2 antibody is effective, at least in part, because it prevents HSV-2 evasion from complement. Immunization with gC-2 also produced neutralizing antibodies that were active in the absence of complement; however, the neutralizing titers were higher when complement was present, with the highest titers in animals immunized with both antigens. Animals immunized with the gC-2-plus-gD-2 combination had robust CD4+ T-cell responses to each immunogen. Multiple disease parameters were evaluated in mice and guinea pigs immunized with gC-2 alone, gD-2 alone, or both antigens. In general, gD-2 outperformed gC-2; however, the gC-2-plus-gD-2 combination outperformed gD-2 alone, particularly in protecting dorsal root ganglia in mice and reducing recurrent vaginal shedding of HSV-2 DNA in guinea pigs. Therefore, the gC-2 subunit antigen enhances a gD-2 subunit vaccine by stimulating a CD4+ T-cell response, by producing neutralizing antibodies that are effective in the absence and presence of complement, and by blocking immune evasion domains that inhibit complement activation.

  19. Radiation Combined Injury: DNA Damage, Apoptosis, and Autophagy (United States)


    the course of their disease (5) represents another significant source of exposure as normal tissues are subjected to radiation injury. Those charged...received thermal burns concurrent with radiation injury, (26, 35). At the Chernobyl reactor meltdown, 10% of 237 victims exposed to radiation received...injections, orally administered drugs, and perhaps subcutaneous injections (39) may be the most complex treatments available to mass casualty victims

  20. The binding of in vitro synthesized adenovirus DNA binding protein to single-stranded DNA is stimulated by zinc ions

    NARCIS (Netherlands)

    Vos, H.L.; Lee, F.M. van der; Sussenbach, J.S.


    We have synthesized wild type DNA binding protein (DBP) of adenovirus type 5 (Ad5) and several truncated forms of this protein by a combination of in vitro transcription and translation. The proteins obtained were tested for binding to a single-stranded DNA-cellulose column. It could be shown that f

  1. DNA replication and cancer

    DEFF Research Database (Denmark)

    Boyer, Anne-Sophie; Walter, David; Sørensen, Claus Storgaard


    A dividing cell has to duplicate its DNA precisely once during the cell cycle to preserve genome integrity avoiding the accumulation of genetic aberrations that promote diseases such as cancer. A large number of endogenous impacts can challenge DNA replication and cells harbor a battery of pathways...... to promote genome integrity during DNA replication. This includes suppressing new replication origin firing, stabilization of replicating forks, and the safe restart of forks to prevent any loss of genetic information. Here, we describe mechanisms by which oncogenes can interfere with DNA replication thereby...... causing DNA replication stress and genome instability. Further, we describe cellular and systemic responses to these insults with a focus on DNA replication restart pathways. Finally, we discuss the therapeutic potential of exploiting intrinsic replicative stress in cancer cells for targeted therapy....

  2. DNA supercoiling during transcription (United States)

    Ma, Jie; Wang, Michelle D.


    The twin-supercoiled-domain model describes how transcription can drive DNA supercoiling, and how DNA supercoiling, in turn plays an important role in regulating gene transcription. In vivo and in vitro experiments have disclosed many details of the complex interactions in this relationship, and recently new insights have been gained with the help of genome-wide DNA supercoiling mapping techniques and single molecule methods. This review summarizes the general mechanisms of the interplay between DNA supercoiling and transcription, considers the biological implications, and focuses on recent important discoveries and technical advances in this field. We highlight the significant impact of DNA supercoiling in transcription, but also more broadly in all processes operating on DNA.

  3. DNA topology and transcription. (United States)

    Kouzine, Fedor; Levens, David; Baranello, Laura


    Chromatin is a complex assembly that compacts DNA inside the nucleus while providing the necessary level of accessibility to regulatory factors conscripted by cellular signaling systems. In this superstructure, DNA is the subject of mechanical forces applied by variety of molecular motors. Rather than being a rigid stick, DNA possesses dynamic structural variability that could be harnessed during critical steps of genome functioning. The strong relationship between DNA structure and key genomic processes necessitates the study of physical constrains acting on the double helix. Here we provide insight into the source, dynamics, and biology of DNA topological domains in the eukaryotic cells and summarize their possible involvement in gene transcription. We emphasize recent studies that might inspire and impact future experiments on the involvement of DNA topology in cellular functions.

  4. DNA profiles from fingermarks. (United States)

    Templeton, Jennifer E L; Linacre, Adrian


    Criminal investigations would be considerably improved if DNA profiles could be routinely generated from single fingermarks. Here we report a direct DNA profiling method that was able to generate interpretable profiles from 71% of 170 fingermarks. The data are based on fingermarks from all 5 digits of 34 individuals. DNA was obtained from the fingermarks using a swab moistened with Triton-X, and the fibers were added directly to one of two commercial DNA profiling kits. All profiles were obtained without increasing the number of amplification cycles; therefore, our method is ideally suited for adoption by the forensic science community. We indicate the use of the technique in a criminal case in which a DNA profile was generated from a fingermark on tape that was wrapped around a drug seizure. Our direct DNA profiling approach is rapid and able to generate profiles from touched items when current forensic practices have little chance of success.

  5. Hysteresis in pressure-driven DNA denaturation.

    Directory of Open Access Journals (Sweden)

    Enrique Hernández-Lemus

    Full Text Available In the past, a great deal of attention has been drawn to thermal driven denaturation processes. In recent years, however, the discovery of stress-induced denaturation, observed at the one-molecule level, has revealed new insights into the complex phenomena involved in the thermo-mechanics of DNA function. Understanding the effect of local pressure variations in DNA stability is thus an appealing topic. Such processes as cellular stress, dehydration, and changes in the ionic strength of the medium could explain local pressure changes that will affect the molecular mechanics of DNA and hence its stability. In this work, a theory that accounts for hysteresis in pressure-driven DNA denaturation is proposed. We here combine an irreversible thermodynamic approach with an equation of state based on the Poisson-Boltzmann cell model. The latter one provides a good description of the osmotic pressure over a wide range of DNA concentrations. The resulting theoretical framework predicts, in general, the process of denaturation and, in particular, hysteresis curves for a DNA sequence in terms of system parameters such as salt concentration, density of DNA molecules and temperature in addition to structural and configurational states of DNA. Furthermore, this formalism can be naturally extended to more complex situations, for example, in cases where the host medium is made up of asymmetric salts or in the description of the (helical-like charge distribution along the DNA molecule. Moreover, since this study incorporates the effect of pressure through a thermodynamic analysis, much of what is known from temperature-driven experiments will shed light on the pressure-induced melting issue.

  6. Tracking earthworm communities from soil DNA. (United States)

    Bienert, Friederike; De Danieli, Sébastien; Miquel, Christian; Coissac, Eric; Poillot, Carole; Brun, Jean-Jacques; Taberlet, Pierre


    Earthworms are known for their important role within the functioning of an ecosystem, and their diversity can be used as an indicator of ecosystem health. To date, earthworm diversity has been investigated through conventional extraction methods such as handsorting, soil washing or the application of a mustard solution. Such techniques are time consuming and often difficult to apply. We showed that combining DNA metabarcoding and next-generation sequencing facilitates the identification of earthworm species from soil samples. The first step of our experiments was to create a reference database of mitochondrial DNA (mtDNA) 16S gene for 14 earthworm species found in the French Alps. Using this database, we designed two new primer pairs targeting very short and informative DNA sequences (about 30 and 70 bp) that allow unambiguous species identification. Finally, we analysed extracellular DNA taken from soil samples in two localities (two plots per locality and eight samples per plot). The two short metabarcode regions led to the identification of a total of eight earthworm species. The earthworm communities identified by the DNA-based approach appeared to be well differentiated between the two localities and are consistent with results derived from inventories collected using the handsorting method. The possibility of assessing earthworm communities from hundreds or even thousands of localities through the use of extracellular soil DNA will undoubtedly stimulate further ecological research on these organisms. Using the same DNA extracts, our study also illustrates the potential of environmental DNA as a tool to assess the diversity of other soil-dwelling animal taxa.

  7. Isothermal hybridization kinetics of DNA assembly of two-dimensional DNA origami. (United States)

    Song, Jie; Zhang, Zhao; Zhang, Shuai; Liu, Lei; Li, Qiang; Xie, Erqing; Gothelf, Kurt Vesterager; Besenbacher, Flemming; Dong, Mingdong


    The Watson-Crick base-pairing with specificity and predictability makes DNA molecules suitable for building versatile nanoscale structures and devices, and the DNA origami method enables researchers to incorporate more complexities into DNA-based devices. Thermally controlled atomic force microscopy in combination with nanomechanical spectroscopy with forces controlled in the pico Newton (pN) range as a novel technique is introduced to directly investigate the kinetics of multistrand DNA hybridization events on DNA origami nanopores under defined isothermal conditions. For the synthesis of DNA nanostructures under isothermal conditions at 60 °C, a higher hybridization rate, fewer defects, and a higher stability are achieved compared to room-temperature studies. By quantifying the assembly times for filling pores in origami structures at several constant temperatures, the fill factors show a consistent exponential increase over time. Furthermore, the local hybridization rate can be accelerated by adding a higher concentration of the staples. The new insight gained on the kinetics of staple-scaffold hybridization on the synthesis of two dimensional DNA origami structures may open up new routes and ideas for designing DNA assembly systems with increased potential for their application.

  8. Binary electrokinetic separation of target DNA from background DNA primers.

    Energy Technology Data Exchange (ETDEWEB)

    James, Conrad D.; Derzon, Mark Steven


    This report contains the summary of LDRD project 91312, titled ''Binary Electrokinetic Separation of Target DNA from Background DNA Primers''. This work is the first product of a collaboration with Columbia University and the Northeast BioDefense Center of Excellence. In conjunction with Ian Lipkin's lab, we are developing a technique to reduce false positive events, due to the detection of unhybridized reporter molecules, in a sensitive and multiplexed detection scheme for nucleic acids developed by the Lipkin lab. This is the most significant problem in the operation of their capability. As they are developing the tools for rapidly detecting the entire panel of hemorrhagic fevers this technology will immediately serve an important national need. The goal of this work was to attempt to separate nucleic acid from a preprocessed sample. We demonstrated the preconcentration of kilobase-pair length double-stranded DNA targets, and observed little preconcentration of 60 base-pair length single-stranded DNA probes. These objectives were accomplished in microdevice formats that are compatible with larger detection systems for sample pre-processing. Combined with Columbia's expertise, this technology would enable a unique, fast, and potentially compact method for detecting/identifying genetically-modified organisms and multiplexed rapid nucleic acid identification. Another competing approach is the DARPA funded IRIS Pharmaceutical TIGER platform which requires many hours for operation, and an 800k$ piece of equipment that fills a room. The Columbia/SNL system could provide a result in 30 minutes, at the cost of a few thousand dollars for the platform, and would be the size of a shoebox or smaller.

  9. DNA Media Storage



    In 1994, University of Southern California computer scientist Dr. Leonard Adelman solved the Hamiltonian Path Problem using DNA as a computational mechanism. He proved the principle that DNA computing could be used to solve computationally complex problems. Because of the limitations in discovery time, resource requirements, and sequence mismatches, DNA computing has not yet become a commonly accepted practice. However, advancements are continually being discovered that are evolving the field...

  10. Disentangling DNA molecules (United States)

    Vologodskii, Alexander


    The widespread circular form of DNA molecules inside cells creates very serious topological problems during replication. Due to the helical structure of the double helix the parental strands of circular DNA form a link of very high order, and yet they have to be unlinked before the cell division. DNA topoisomerases, the enzymes that catalyze passing of one DNA segment through another, solve this problem in principle. However, it is very difficult to remove all entanglements between the replicated DNA molecules due to huge length of DNA comparing to the cell size. One strategy that nature uses to overcome this problem is to create the topoisomerases that can dramatically reduce the fraction of linked circular DNA molecules relative to the corresponding fraction at thermodynamic equilibrium. This striking property of the enzymes means that the enzymes that interact with DNA only locally can access their topology, a global property of circular DNA molecules. This review considers the experimental studies of the phenomenon and analyzes the theoretical models that have been suggested in attempts to explain it. We describe here how various models of enzyme action can be investigated computationally. There is no doubt at the moment that we understand basic principles governing enzyme action. Still, there are essential quantitative discrepancies between the experimental data and the theoretical predictions. We consider how these discrepancies can be overcome.


    Energy Technology Data Exchange (ETDEWEB)



    During this year we performed two major projects: I. We developed a detailed theoretical model which complements our experiments on surface DNA electrophoresis. We found that it was possible to enhance the separation of DNA chains by imposing a chemical nanoscale pattern on the surface. This approach utilized the surface interaction effect of the DNA chains with the substrate and is a refinement to our previous method in which DNA chains were separated on homogeneous flat surfaces. By introducing the nano-patterns on the surface, the conformational changes of DNA chains of different lengths can be amplified, which results in the different friction strengths with the substrate surface. Our results also show that, when compared to the DNA electrophoresis performed on homogeneous flat surfaces, nanopatterned surfaces offer a larger window in choosing different surface interactions to achieve separation. II. In collaboration with a large international manufacturer of skin care products we also embarked on a project involving photo toxicity of titanium dioxide nanoparticles, which are a key ingredient in sunscreen and cosmetic lotions. The results clearly implicated the nanoparticles in catalyzing damage to chromosomal DNA. We then used this knowledge to develop a polymer/anti-oxidant coating which prevented the photocatalytic reaction on DNA while still retaining the UV absorptive properties of the nanoparticles. The standard gel electrophoresis was not sufficient in determining the extent of the DNA damage. The conclusions of this study were based predominantly on analysis obtained with the surface electrophoresis method.

  12. Disentangling DNA molecules. (United States)

    Vologodskii, Alexander


    The widespread circular form of DNA molecules inside cells creates very serious topological problems during replication. Due to the helical structure of the double helix the parental strands of circular DNA form a link of very high order, and yet they have to be unlinked before the cell division. DNA topoisomerases, the enzymes that catalyze passing of one DNA segment through another, solve this problem in principle. However, it is very difficult to remove all entanglements between the replicated DNA molecules due to huge length of DNA comparing to the cell size. One strategy that nature uses to overcome this problem is to create the topoisomerases that can dramatically reduce the fraction of linked circular DNA molecules relative to the corresponding fraction at thermodynamic equilibrium. This striking property of the enzymes means that the enzymes that interact with DNA only locally can access their topology, a global property of circular DNA molecules. This review considers the experimental studies of the phenomenon and analyzes the theoretical models that have been suggested in attempts to explain it. We describe here how various models of enzyme action can be investigated computationally. There is no doubt at the moment that we understand basic principles governing enzyme action. Still, there are essential quantitative discrepancies between the experimental data and the theoretical predictions. We consider how these discrepancies can be overcome.

  13. DNA Microarray Technique

    Directory of Open Access Journals (Sweden)

    Thakare SP


    Full Text Available DNA Microarray is the emerging technique in Biotechnology. The many varieties of DNA microarray or DNA chip devices and systems are described along with their methods for fabrication and their use. It also includes screening and diagnostic applications. The DNA microarray hybridization applications include the important areas of gene expression analysis and genotyping for point mutations, single nucleotide polymorphisms (SNPs, and short tandem repeats (STRs. In addition to the many molecular biological and genomic research uses, this review covers applications of microarray devices and systems for pharmacogenomic research and drug discovery, infectious and genetic disease and cancer diagnostics, and forensic and genetic identification purposes.

  14. DNA Based Molecular Scale Nanofabrication (United States)


    water adsorption on DNA origami template and its impact on DNA- mediated chemical reactions. We also extended the concept of DNA- mediated reaction to...addition, we have expanded our efforts to include DNA- mediated HF etching of SiÜ2, DNA- mediated nanoimprinting lithography, DNA-based patterning of self...detailed kinetics study of DNA- mediated chemical reactions. Examples of such reactions include chemical vapor deposition (CVD) of inorganic oxide and HF

  15. Liquid-based cytology combined HPV-DNA genotyping in cervical cancer screening%液基细胞学检查联合人乳头瘤病毒基因分型检测在宫颈癌筛查中的应用

    Institute of Scientific and Technical Information of China (English)

    刘汉忠; 杨继洲; 肖兰; 卢叶; 戴一菲; 王岚


    目的 探讨液基细胞学检查(TCT)联合人乳头瘤病毒基因(HPV-DNA)分型检测在宫颈癌筛查中的应用价值.方法 对28 524例女性患者进行TCT检测,其中5 932例TCT诊断为不能明确意义的非典型鳞状细胞(ASCUS)及以上的患者均行HPV-DNA分型检测及宫颈活检,分析TCT和HPV感染与宫颈癌及癌前病变的相关性.结果 共检测样本28 524例,其中良性病变22 592例(79.20%),ASCUS 4 824例(16.91%),鳞状上皮内低度病变(LSIL) 776例(2.72%),鳞状上皮内高度病变(HSIL) 316例(1.11%),鳞状细胞癌(SCC) 16例(0.06%).HSIL符合率为97.47%(308/316例),SCC符合率为100%(16/16例).HPV-DNA分型检测5 932例,其中阳性1 486例,阳性率为25.05%.TCT诊断与活检结果比较,良性病变与CINⅠ、CINⅡ、CINⅢ比较差异有统计学意义(P<0.01); CINⅠ、CINⅡ、CINⅢ、SCC间比较差异有统计学意义(P<0.01).宫颈活检结果与HPV感染在炎症及CINⅠ、CINⅡ、CINⅢ、SCC组间比较差异有统计学意义(P<0.01).结论 TCT与活检,特别是针对高级病变及癌,符合率较高,特异性较强.TCT与HPV-DNA分型检测对诊断宫颈癌及癌前病变具有敏感、特异和早于形态学改变的特点,具有较高的临床应用价值和推广前景.%Objective To investigate the value of the liquid-based cytology (TCT) joint HPV-DNA genotyping in cervical cancer screening.Methods Liquid-based cytology (TCT) combined HPV-DNA genotyping,and TCT were detected in 28 524 women,including 5 932 of TCT cytological diagnosis of ASCUS or more patients underwent genotyping of HPV-DNA detection and cervical biopsy,TCT and HPV infection and cervical cancer and precancerous lesions to cervical biopsy results confirmed standard.Results The total number of samples tested were 28 524 cases.Benign reactive changes were 22 592 cases (79.20%),ASCUS 4 824 cases (16.91%),LSIL 776 cases (2.72 %),HSIL 316 cases (1.11%),and the SCC 16 cases (0.06 %),in which

  16. PNA Directed Sequence Addressed Self-Assembly of DNA Nanostructures (United States)

    Nielsen, Peter E.


    Peptide nucleic acids (PNA) can be designed to target duplex DNA with very high sequence specificity and efficiency via various binding modes. We have designed three domain PNA clamps, that bind stably to predefined decameric homopurine targets in large dsDNA molecules and via a third PNA domain sequence specifically recognize another PNA oligomer. We describe how such three domain PNAs have utility for assembling dsDNA grid and clover leaf structures, and in combination with SNAP-tag technology of protein dsDNA structures.

  17. Mitochondrial DNA, restoring Beethovens music. (United States)

    Merheb, Maxime; Vaiedelich, Stéphane; Maniguet, Thiérry; Hänni, Catherine


    Great ancient composers have endured many obstacles and constraints which are very difficult to understand unless we perform the restoration process of ancient music. Species identification in leather used during manufacturing is the key step to start such a restoration process in order to produce a facsimile of a museum piano. Our study reveals the species identification in the leather covering the hammer head in a piano created by Erard in 1802. This is the last existing piano similar to the piano that Beethoven used with its leather preserved in its original state. The leather sample was not present in a homogeneous piece, yet combined with glue. Using a DNA extraction method that avoids PCR inhibitors; we discovered that sheep and cattle are the origin of the combination. To identify the species in the leather, we focused on the amounts of mitochondrial DNA in both leather and glue and results have led us to the conclusion that the leather used to cover the hammer head in this piano was made of cattle hide.

  18. DNA barcoding, phylogenetic relationships and speciation of snappers (genus Lutjanus)

    Institute of Scientific and Technical Information of China (English)


    The phylogenetic relationships of 13 snapper species from the South China Sea have been established using the combined DNA sequences of three full-length mitochondrial genes (COI, COII and CYTB) and two partial nuclear genes (RAG1, RAG2). The 13 species (genus Lutjanus) were selected after DNA barcoding 72 individuals, representing 20 species. Our study suggests that although DNA barcoding aims to develop species identification systems, it may also be useful in the construction of phylogenies by aiding the selection of taxa. Combined mitochondrial and nuclear gene data has an advantage over an individual dataset because of its higher resolving power.

  19. Hierarchical-Multiplex DNA Patterns Mediated by Polymer Brush Nanocone Arrays That Possess Potential Application for Specific DNA Sensing. (United States)

    Liu, Wendong; Liu, Xueyao; Ge, Peng; Fang, Liping; Xiang, Siyuan; Zhao, Xiaohuan; Shen, Huaizhong; Yang, Bai


    This paper provides a facile and cost-efficient method to prepare single-strand DNA (ssDNA) nanocone arrays and hierarchical DNA patterns that were mediated by poly(2-hydroxyethyl methacrylate) (PHEMA) brush. The PHEMA brush nanocone arrays with different morphology and period were fabricated via colloidal lithography. The hierarchical structure was prepared through the combination of colloidal lithography and traditional photolithography. The DNA patterns were easily achieved via grafting the amino group modified ssDNA onto the side chain of polymer brush, and the anchored DNA maintained their reactivity. The as-prepared ssDNA nanocone arrays can be applied for target DNA sensing with the detection limit reaching 1.65 nM. Besides, with the help of introducing microfluidic ideology, the hierarchical-multiplex DNA patterns on the same substrate could be easily achieved with each kind of pattern possessing one kind of ssDNA, which are promising surfaces for the preparation of rapid, visible, and multiplex DNA sensors.

  20. Crosslinking of DNA repair and replication proteins to DNA in cells treated with 6-thioguanine and UVA. (United States)

    Gueranger, Quentin; Kia, Azadeh; Frith, David; Karran, Peter


    The DNA of patients taking immunosuppressive and anti-inflammatory thiopurines contains 6-thioguanine (6-TG) and their skin is hypersensitive to ultraviolet A (UVA) radiation. DNA 6-TG absorbs UVA and generates reactive oxygen species that damage DNA and proteins. Here, we show that the DNA damage includes covalent DNA-protein crosslinks. An oligonucleotide containing a single 6-TG is photochemically crosslinked to cysteine-containing oligopeptides by low doses of UVA. Crosslinking is significantly more efficient if guanine sulphonate (G(SO3))--an oxidized 6-TG and a previously identified UVA photoproduct--replaces 6-TG, suggesting that G(SO3) is an important reaction intermediate. Crosslinking occurs via oligopeptide sulphydryl and free amino groups. The oligonucleotide-oligopeptide adducts are heat stable but are partially reversed by reducing treatments. UVA irradiation of human cells containing DNA 6-TG induces extensive heat- and reducing agent-resistant covalent DNA-protein crosslinks and diminishes the recovery of some DNA repair and replication proteins from nuclear extracts. DNA-protein crosslinked material has an altered buoyant density and can be purified by banding in cesium chloride (CsCl) gradients. PCNA, the MSH2 mismatch repair protein and the XPA nucleotide excision repair (NER) factor are among the proteins detectable in the DNA-crosslinked material. These findings suggest that the 6-TG/UVA combination might compromise DNA repair by sequestering essential proteins.

  1. Clinical value of TCT combined with HPV-DNA detection in cervical cancer screening%液基薄层细胞学联合 HPV-DNA检测对宫颈癌患者筛查的临床价值

    Institute of Scientific and Technical Information of China (English)



    Objective:To explore clinical value ThinPrep cytology test ( TCT) and HPV detection in cervical cancer screen-ing. Methods:The clinical data of the patients in the screening of cervical precancerous lesions were collected. Each patient was given TCT combined with HPV detection. Finally, after colposcopy cervical biopsy, the sensitivity, accuracy and false positive rate of single TCT, single HPV and TCT combined with HPV in the diagnosis of chronic cervical inflammation, cervical precancerous lesions and cervical cancer were compared. Results:The cervical cancer and precancerous lesions screening under colposcopy biopsy was done in 360 patients. Among the 3 screening methods, the combined application of TCT and HPV had the highest sensitivity and specificity, and could be used for diagnosing severe atypical hyperplasia ( CIN-III) and cervical carcinoma without missed diagnosis;however, it might miss some moderate dysplasia ( CIN-II) and mild atypical hyperplasia ( CIN-I) patients. Conclusions:The TCT combined with HPV-DNA detection can be used actively in the cervical precancerous lesions screening, and improve the accuracy of clinical diagno-sis. Moreover, combined with colposcopy biopsy of cervical cancer and precancerous lesions, it can provide a diagnostic basis for the clinical treatment, and is worthy of clinical application.%目的::探讨液基薄层细胞学与HPV检测联合应用后在宫颈癌患者筛查中的临床应用价值。方法:分析行宫颈癌前病变筛查的患者共360例临床资料,每位患者给予薄层液基细胞学联合HPV检测,最后经阴道镜下宫颈活检,比较单独TCT检查、单独HPV检查及两种检查联合检测在诊断患者宫颈慢性炎症、宫颈癌前病变及宫颈癌的敏感程度、准确性和假阳性率。结果:宫颈癌及癌前病变筛查患者,行阴道镜下活检的患者360例。3种筛选方法中,联合应用TCT及HPV的敏感性、特异性最

  2. DNA extraction from Ascaris suum muscle tissue


    Di Mito, Carmela; Betschart, Bruno


    A new method for the extraction of DNA from Ascaris suum muscle has been developed. It combines a standard SDS-based extraction with a plant DNA extraction procedure. The use of SDS and proteinase K allows the elimination of proteins, while CTAB and polyclar AT eliminate glycogen and polyphenols. The DNA thus obtained can easily be digested by endonucleases and amplified by PCR.

  3. The roles of adenoviral vectors and donor DNA structures on genome editing

    NARCIS (Netherlands)

    Holkers, Maarten


    Accurate and efficient genome editing is primarily dependent on the generation of a sequence-specific, genomic double-stranded DNA break (DSB) combined with the introduction of an exogenous DNA template into target cells. The exogenous template, called donor DNA, normally contains the foreign sequen

  4. Trans-dichlorooxovandium (IV) complex as a novel photoinducible DNA interstrand crosslinker for cancer therapy

    DEFF Research Database (Denmark)

    Somyajit, Kumar; Banik, Bhabatosh; Saxena, Sneha


    -dichlorooxovanadium (IV) complex of pyrenyl terpyridine (VDC) is a novel photoinducible DNA crosslinking agent. By a combination of in vitro and ex vivo experiments including plasmid-based assays, we find that VDC forms monoadducts on the DNA and can be activated by UV-A and visible light to generate DNA interstrand...

  5. DNA Polymerase θ: Duct Tape and Zip Ties for a Fragile Genome. (United States)

    Willis, Nicholas A; Scully, Ralph


    Using a combination of genetics and cellular DNA rejoining assays, in this issue of Molecular Cell, Wyatt et al. (2016) demonstrate a critical role for mammalian DNA polymerase θ in the rejoining of DNA ends that are poor substrates for classical non-homologous end joining.

  6. DNA-cell conjugates (United States)

    Hsiao, Shih-Chia; Francis, Matthew B.; Bertozzi, Carolyn; Mathies, Richard; Chandra, Ravi; Douglas, Erik; Twite, Amy; Toriello, Nicholas; Onoe, Hiroaki


    The present invention provides conjugates of DNA and cells by linking the DNA to a native functional group on the cell surface. The cells can be without cell walls or can have cell walls. The modified cells can be linked to a substrate surface and used in assay or bioreactors.

  7. Extended DNA Tile Actuators

    DEFF Research Database (Denmark)

    Kristiansen, Martin; Kryger, Mille; Zhang, Zhao


    A dynamic linear DNA tile actuator is expanded to three new structures of higher complexity. The original DNA actuator was constructed from a central roller strand which hybridizes with two piston strands by forming two half-crossover junctions. A linear expansion of the actuator is obtained...

  8. DNA sequences encoding erythropoietin

    Energy Technology Data Exchange (ETDEWEB)

    Lin, F.K.


    A purified and isolated DNA sequence is described consisting essentially of a DNA sequence encoding a polypeptide having an amino acid sequence sufficiently duplicative of that of erythropoietin to allow possession of the biological property of causing bone marrow cells to increase production of reticulocytes and red blood cells, and to increase hemoglobin synthesis or iron uptake.

  9. Characterization of muntjac DNA

    Energy Technology Data Exchange (ETDEWEB)

    Davis, R.C.


    Sister chromatid exchange (SCE) in muntjac chromosomes is generally proportional to the chromosomal DNA content, but the SCE frequency is reduced in the heterochromatic neck region of the X chromosome. The physical properties of muntjac DNA and the kinetics of repair of UV damage in muntjac heterochromatin and euchromatin were examined and compared with the distribution of sister chromatid exchange.

  10. Workshop on DNA repair.

    NARCIS (Netherlands)

    A.R. Lehmann (Alan); J.H.J. Hoeijmakers (Jan); A.A. van Zeeland (Albert); C.M.P. Backendorf (Claude); B.A. Bridges; A. Collins; R.P.D. Fuchs; G.P. Margison; R. Montesano; E. Moustacchi; A.T. Natarajan; M. Radman; A. Sarasin; E. Seeberg; C.A. Smith; M. Stefanini (Miria); L.H. Thompson; G.P. van der Schans; C.A. Weber (Christine); M.Z. Zdzienika


    textabstractA workshop on DNA repair with emphasis on eukaryotic systems was held, under the auspices of the EC Concerted Action on DNA Repair and Cancer, at Noordwijkerhout (The Netherlands) 14-19 April 1991. The local organization of the meeting was done under the auspices of the Medical Genetic C

  11. Recombinant DNA for Teachers. (United States)

    Duvall, James G., III


    A science teacher describes his experience at a workshop to learn to teach the Cold Spring Harbor DNA Science Laboratory Protocols. These protocols lead students through processes for taking E. coli cells and transforming them into a new antibiotic resistant strain. The workshop featured discussions of the role of DNA recombinant technology in…

  12. DNA repair protocols

    DEFF Research Database (Denmark)

    Bjergbæk, Lotte

    In its 3rd edition, this Methods in Molecular Biology(TM) book covers the eukaryotic response to genomic insult including advanced protocols and standard techniques in the field of DNA repair. Offers expert guidance for DNA repair, recombination, and replication. Current knowledge of the mechanisms...... that regulate DNA repair has grown significantly over the past years with technology advances such as RNA interference, advanced proteomics and microscopy as well as high throughput screens. The third edition of DNA Repair Protocols covers various aspects of the eukaryotic response to genomic insult including...... recent advanced protocols as well as standard techniques used in the field of DNA repair. Both mammalian and non-mammalian model organisms are covered in the book, and many of the techniques can be applied with only minor modifications to other systems than the one described. Written in the highly...

  13. Whose DNA is this?

    DEFF Research Database (Denmark)

    Taroni, Franco; Biedermann, Alex; Vuille, Joëlle


    This communication seeks to draw the attention of researchers and practitioners dealing with forensic DNA profiling analyses to the following question: is a scientist's report, offering support to a hypothesis according to which a particular individual is the source of DNA detected during...... evoked during the international conference "The hidden side of DNA profiles. Artifacts, errors and uncertain evidence" held in Rome (April 27th to 28th, 2012). Indeed, despite the fact that this conference brought together some of the world's leading forensic DNA specialists, it appeared clearly...... talk considerably different languages. It thus is fundamental to address this issue of communication about results of forensic DNA analyses, and open a dialogue with practicing non-scientists at large who need to make meaningful use of scientific results to approach and help solve judicial cases...

  14. Whose DNA is this?

    DEFF Research Database (Denmark)

    Taroni, Franco; Biedermann, Alex; Vuille, Joëlle;


    This communication seeks to draw the attention of researchers and practitioners dealing with forensic DNA profiling analyses to the following question: is a scientist's report, offering support to a hypothesis according to which a particular individual is the source of DNA detected during...... evoked during the international conference "The hidden side of DNA profiles. Artifacts, errors and uncertain evidence" held in Rome (April 27th to 28th, 2012). Indeed, despite the fact that this conference brought together some of the world's leading forensic DNA specialists, it appeared clearly....... This paper intends to emphasize the actuality of this topic and suggest beneficial ways ahead towards a more reasoned use of forensic DNA in criminal proceedings....

  15. Straightforward Procedure for Laboratory Production of DNA Ladder

    Directory of Open Access Journals (Sweden)

    Vo Thi Thuong Lan


    Full Text Available DNA ladder is commonly used to determine the size of DNA fragments by electrophoresis in routine molecular biology laboratories. In this study, we report a new procedure to prepare a DNA ladder that consists of 10 fragments from 100 to 1000 bp. This protocol is a combination of routinely employed methods: cloning, PCR, and partial digestion with restriction enzymes. DNA fragments of 100 bp with unique restriction site at both ends were self-ligated to create a tandem repeat. Once being cloned, the tandem repeat was rapidly amplified by PCR and partially digested by restriction enzymes to produce a ladder containing multimers of the repeated DNA fragments. Our procedure for production of DNA ladder could be simple, time saving, and inexpensive in comparison with current ones widely used in most laboratories.

  16. Diverse Applications of Environmental DNA Methods in Parasitology. (United States)

    Bass, David; Stentiford, Grant D; Littlewood, D T J; Hartikainen, Hanna


    Nucleic acid extraction and sequencing of genes from organisms within environmental samples encompasses a variety of techniques collectively referred to as environmental DNA or 'eDNA'. The key advantages of eDNA analysis include the detection of cryptic or otherwise elusive organisms, large-scale sampling with fewer biases than specimen-based methods, and generation of data for molecular systematics. These are particularly relevant for parasitology because parasites can be difficult to locate and are morphologically intractable and genetically divergent. However, parasites have rarely been the focus of eDNA studies. Focusing on eukaryote parasites, we review the increasing diversity of the 'eDNA toolbox'. Combining eDNA methods with complementary tools offers much potential to understand parasite communities, disease risk, and parasite roles in broader ecosystem processes such as food web structuring and community assembly.

  17. DNA base excision repair nanosystem engineering: model development. (United States)

    Sokhansanj, B A


    DNA base damage results from a combination of endogenous sources, (normal metabolism, increased metabolism due to obesity, stress from diseases such as arthritis and diabetes, and ischemia) and the environment (ingested toxins, ionizing radiation, etc.). If unrepaired DNA base damage can lead to diminished cell function, and potentially diseases and eventually mutations that lead to cancer. Sophisticated DNA repair mechanisms have evolved in all living cells to preserve the integrity of inherited genetic information and transcriptional control. Understanding a system like DNA repair is greatly enhanced by using engineering methods, in particular modeling interactions and using predictive simulation to analyze the impact of perturbations. We describe the use of such a "nanosystem engineering" approach to analyze the DNA base excision repair pathway in human cells, and use simulation to predict the impact of varying enzyme concentration on DNA repair capacity.

  18. Osmotic pressure: resisting or promoting DNA ejection from phage

    CERN Document Server

    Jeembaeva, Meerim; Larsson, Frida; Evilevitch, Alex


    Recent in vitro experiments have shown that DNA ejection from bacteriophage can be partially stopped by surrounding osmotic pressure when ejected DNA is digested by DNase I on the course of ejection. We argue in this work by combination of experimental techniques (osmotic suppression without DNaseI monitored by UV absorbance, pulse-field electrophoresis, and cryo-EM visualization) and simple scaling modeling that intact genome (i.e. undigested) ejection in a crowded environment is, on the contrary, enhanced or eventually complete with the help of a pulling force resulting from DNA condensation induced by the osmotic stress itself. This demonstrates that in vivo, the osmotically stressed cell cytoplasm will promote phage DNA ejection rather than resisting it. The further addition of DNA-binding proteins under crowding conditions is shown to enhance the extent of ejection. We also found some optimal crowding conditions for which DNA content remaining in the capsid upon ejection is maximum, which correlates well...

  19. Specific hydrolysis of DNA by Ce4+-ODN hybrid

    Institute of Scientific and Technical Information of China (English)

    SHEN; Hebai; ZHOU; Wenjun; YANG; Yongtao; ZHANG; Feng


    The cerium complex bound to the derivative of oligoDNA has been synthesized successfully that can hydrolyze DNA with sequence-specificity. The synthesized derivative of oligoDNA, 5′-EDTA-P-10 mers ODN, was demonstrated by HPLC. The fluorescence spectrum of Tb3+ was detected after its interaction with the hybrid of 10-mers ODN and 26-mers ODN and the results show that the artificial endo-enzyme can recognize and combine firmly with the substrate DNA. The electrophorogram shows that the cerium-oligoDNA hybrid can specifically hydrolyze its substrate DNA and the cleavage site of this hydrolysis reaction is also discussed. This artificial nuclease can be widely used in molecular biology and genetic engineering as one kind of endo-enzyme.

  20. ENA多肽抗体谱检测结合抗ds-DNA及补体C3测定在SLE诊断上的应用%Spectrum of ENA polypeptide antibodies combined with anti ds-DNA and C3 determination in the diagnosis of systemic lupus erythematosus

    Institute of Scientific and Technical Information of China (English)

    吕春兰; 都青; 杨荣生; 曹宪华


    in orther rheumatic diseases,the specificity is relatively high. Anti- SSA, anti- UIRNP in SLE was 36.8%, 27.6% , and orther rheumatic diseases are also detected,specificity is relatively low. In other rheumatic diseases the positive rate about anti SSA, anti SSB, anti UIRNP were 50 %, 43 %,25% respectively in SS;The positive rate about anti SSA.anti Jo I were 25%,25% respectively in PPS;The positive rates about anti SSA,anti UIRNP,anti-Jo-1, antiDM53 were 25%,25%,12. 5%,37. 5% respectively in DM;the positive rates about antiSSA,anti UIRNP,anti-- A/54 were 32.6% ,11.9% ,15.2%respectively in RF. Complement C3 in the determination of SLE values was low,ranging from 0.46 ± 0.12 , compared with orther rheumatic diseases, (P<0.01) significant differences. Conclusion The combination of anti- ENA antibodies, anti, ds- DNA antibodies and complement C3 determination in the diagnosis of SLE have significant clinical significance.

  1. Environmental DNA reflects spatial and temporal jellyfish distribution (United States)

    Fukuda, Miho; Katsuhara, Koki R.; Fujiwara, Ayaka; Hidaka, Shunsuke; Yamamoto, Satoshi; Takahashi, Kohji; Masuda, Reiji


    Recent development of environmental DNA (eDNA) analysis allows us to survey underwater macro-organisms easily and cost effectively; however, there have been no reports on eDNA detection or quantification for jellyfish. Here we present the first report on an eDNA analysis of marine jellyfish using Japanese sea nettle (Chrysaora pacifica) as a model species by combining a tank experiment with spatial and temporal distribution surveys. We performed a tank experiment monitoring eDNA concentrations over a range of time intervals after the introduction of jellyfish, and quantified the eDNA concentrations by quantitative real-time PCR. The eDNA concentrations peaked twice, at 1 and 8 h after the beginning of the experiment, and became stable within 48 h. The estimated release rates of the eDNA in jellyfish were higher than the rates previously reported in fishes. A spatial survey was conducted in June 2014 in Maizuru Bay, Kyoto, in which eDNA was collected from surface water and sea floor water samples at 47 sites while jellyfish near surface water were counted on board by eye. The distribution of eDNA in the bay corresponded with the distribution of jellyfish inferred by visual observation, and the eDNA concentration in the bay was ~13 times higher on the sea floor than on the surface. The temporal survey was conducted from March to November 2014, in which jellyfish were counted by eye every morning while eDNA was collected from surface and sea floor water at three sampling points along a pier once a month. The temporal fluctuation pattern of the eDNA concentrations and the numbers of observed individuals were well correlated. We conclude that an eDNA approach is applicable for jellyfish species in the ocean. PMID:28245277

  2. Left-handed DNA crossovers. Implications for DNA-DNA recognition and structural alterations. (United States)

    Timsit, Y; Shatzky-Schwartz, M; Shakked, Z


    The close approach of DNA segments participates in many biological functions including DNA condensation and DNA processing. Previous crystallographic studies have shown that B-DNA self-fitting by mutual groove-backbone interaction produces right-handed DNA crossovers. These structures have opened new perspectives on the role of close DNA-DNA interactions in the architecture and activity the DNA molecule. In the present study, the analysis of the crystal packing of two B-DNA decamer duplexes d(CCIIICCCGG) and d(CCGCCGGCGG) reveals the existence of new modes of DNA crossing. Symmetric left-handed crossovers are produced by mutual fitting of DNA grooves at the crossing point. New sequence patterns contribute to stabilize longitudinal fitting of the sugar-phosphate backbone into the major groove. In addition, the close approach of DNA segments greatly influences the DNA conformation in a sequence dependent manner. This study provides new insights into the role of DNA sequence and structure in DNA-DNA recognition. In providing detailed molecular views of DNA crossovers of opposite chirality, this study can also help to elucidate the role of symmetry and chirality in the recognition of complex DNA structures by protein dimers or tetramers, such as topoisomerase II and recombinase enzymes. These results are discussed in the context of the possible relationships between DNA condensation and DNA processing.

  3. Simple & Safe Genomic DNA Isolation. (United States)

    Moss, Robert; Solomon, Sondra


    A procedure for purifying DNA using either bacteria or rat liver is presented. Directions for doing a qualitative DNA assay using diphenylamine and a quantitative DNA assay using spectroscopy are included. (KR)

  4. Near-atomic structural model for bacterial DNA replication initiation complex and its functional insights. (United States)

    Shimizu, Masahiro; Noguchi, Yasunori; Sakiyama, Yukari; Kawakami, Hironori; Katayama, Tsutomu; Takada, Shoji


    Upon DNA replication initiation in Escherichia coli, the initiator protein DnaA forms higher-order complexes with the chromosomal origin oriC and a DNA-bending protein IHF. Although tertiary structures of DnaA and IHF have previously been elucidated, dynamic structures of oriC-DnaA-IHF complexes remain unknown. Here, combining computer simulations with biochemical assays, we obtained models at almost-atomic resolution for the central part of the oriC-DnaA-IHF complex. This complex can be divided into three subcomplexes; the left and right subcomplexes include pentameric DnaA bound in a head-to-tail manner and the middle subcomplex contains only a single DnaA. In the left and right subcomplexes, DnaA ATPases associated with various cellular activities (AAA+) domain III formed helices with specific structural differences in interdomain orientations, provoking a bend in the bound DNA. In the left subcomplex a continuous DnaA chain exists, including insertion of IHF into the DNA looping, consistent with the DNA unwinding function of the complex. The intervening spaces in those subcomplexes are crucial for DNA unwinding and loading of DnaB helicases. Taken together, this model provides a reasonable near-atomic level structural solution of the initiation complex, including the dynamic conformations and spatial arrangements of DnaA subcomplexes.

  5. A CLIQUE algorithm using DNA computing techniques based on closed-circle DNA sequences. (United States)

    Zhang, Hongyan; Liu, Xiyu


    DNA computing has been applied in broad fields such as graph theory, finite state problems, and combinatorial problem. DNA computing approaches are more suitable used to solve many combinatorial problems because of the vast parallelism and high-density storage. The CLIQUE algorithm is one of the gird-based clustering techniques for spatial data. It is the combinatorial problem of the density cells. Therefore we utilize DNA computing using the closed-circle DNA sequences to execute the CLIQUE algorithm for the two-dimensional data. In our study, the process of clustering becomes a parallel bio-chemical reaction and the DNA sequences representing the marked cells can be combined to form a closed-circle DNA sequences. This strategy is a new application of DNA computing. Although the strategy is only for the two-dimensional data, it provides a new idea to consider the grids to be vertexes in a graph and transform the search problem into a combinatorial problem.

  6. Recursive construction of perfect DNA molecules and libraries from imperfect oligonucleotides. (United States)

    Linshiz, Gregory; Yehezkel, Tuval Ben; Shapiro, Ehud


    Making faultless complex objects from potentially faulty building blocks is a fundamental challenge in computer engineering, nanotechnology, and synthetic biology. We developed an error-correcting recursive construction procedure that attempts to address this challenge. Making DNA molecules from synthetic oligonucleotides using the procedure described here surpasses existing methods for de novo DNA synthesis in speed, precision, and amenability to automation. It provides for the first time a unified DNA construction platform for combining synthetic and natural DNA fragments, for constructing designer DNA libraries, and for making the faultless long synthetic DNA building blocks needed for de novo genome construction.